Module | Option | Description | Default |
aphid |
absence=X |
Min normalised combined score (arbitrarily assigned to proteins totally absent from samples) |
0.5 |
aphid |
basefile=X |
Text base for output files and resdir |
default based on data file name |
aphid |
combine=X |
Methods for combining different replicates (max,mean,min,geo,full) |
mean |
aphid |
enrcut=X |
Enrichment > X for jack-knifing test |
1.0 |
aphid |
famcut=X |
Percentage identity to be used by GABLAM for clustering |
0.0 |
aphid |
identifier=X |
Column containing protein indentifications |
Identifier |
aphid |
intensity=X |
Column containing intensity values |
logInt |
aphid |
normalise=X |
Scoring strategy for normalising intensity (ppm/shared/none/mwt/frag/count) |
ppm |
aphid |
nr=X |
Level for redundancy removal (gene/pep/fam) |
gene |
aphid |
pepcount=X |
Column containing peptide counts |
rI |
aphid |
replicate=X |
Column heading to identify experimntal replicates |
Replicate |
aphid |
treatment=X |
Column heading to identify different experimental treatment samples (e.g. condition/control) |
Treatment |
badasp |
basefile=X |
Basic 'root' for all files X.* |
By default will use 'root' of seqin=FILE if given or haq_AccNum if qblast |
badasp |
fam=X |
minimum number of families (If 0, no subfam grouping) |
0 |
badasp |
fixpam=X |
PAM distance fixed to X |
100 |
badasp |
groupspec=X |
Species for duplication grouping |
None |
badasp |
i=X |
Sets interactivity (-1 for full auto) |
0 |
badasp |
mfs=X |
minimum family size |
3 |
badasp |
pamcut=X |
Absolute maximum PAM matrix |
1000 |
badasp |
pammax=X |
Initial maximum PAM matrix to generate |
100 |
badasp |
rarecut=X |
Rare aa cut-off |
0.05 |
badasp |
v=X |
Sets verbosity (-1 for silent) |
0 |
badasp |
xpass=X |
How many extra passes to make down & up tree after initial GASP |
1 |
budapest |
basefile=X |
"Base" name for all results files, e.g. X.budapest.tdt |
MASCOT file basename |
budapest |
blastcut=X |
Reduced the number of sequences in HAQESAC runs to X (0 = no reduction) |
50 |
budapest |
minaln=X |
Min length of shared region for FIESTA consensus assembly |
20 |
budapest |
minid=X |
Min identity of shared region for FIESTA consensus assembly |
95.0 |
budapest |
minorf=X |
Min length of ORFs to be considered |
10 |
budapest |
minpep=X |
Minimum number of different peptides mapped to final translation/consensus |
2 |
budapest |
minpolyat=X |
Min length of poly-A/T to be counted. (-1 = ignore all) |
10 |
budapest |
newacc=X |
New base for sequence accession numbers |
'BUD' |
budapest |
spcode=X |
Species code for EST sequences |
None |
budapest |
topblast=X |
Report the top X BLAST results |
10 |
comparimotif_V3 |
ambcut=X |
Max number of choices in ambiguous position before replaced with wildcard (0=use all) |
10 |
comparimotif_V3 |
matchfix=X |
If >0 must exactly match *all* fixed positions in the motifs from: |
0 |
comparimotif_V3 |
minfix=X |
Min number of fixed positions for a motif to contain |
0 |
comparimotif_V3 |
minic=X |
Min information content for a motif (1 fixed position = 1.0) |
2.0 |
comparimotif_V3 |
minpep=X |
Min number of defined positions in a motif |
2 |
comparimotif_V3 |
minshare=X |
Min. number of non-wildcard positions for motifs to share |
2 |
comparimotif_V3 |
mismatches=X |
<= X mismatches of positions can be tolerated |
0 |
comparimotif_V3 |
motdesc=X |
Sets which motifs have description outputs (0-3 as matchfix option) |
3 |
comparimotif_V3 |
normcut=X |
Min. normalised MatchIC for motif match |
0.5 |
comparimotif_V3 |
outstyle=X |
Sets the output style for the resfile |
normal |
diploidocus |
lenfilter=X |
Min read length for filtered subreads |
500 |
diploidocus |
rqfilter=X |
Minimum RQ for output subreads |
0.84 |
extatic |
basefile=X |
Root name for output files. Path will be stripped and resdir used. |
* based on cdna or singleseq |
extatic |
mincds=X |
Minimum CDS lengths to be included in analysis |
0 |
extatic |
minorf=X |
Minimum ORF lengths to be considered |
0 |
extatic |
minutr=X |
Minimum 5' UTR lengths to be included in analysis |
1 |
extatic |
nrflanks=X |
Flanking sequence length (added 5' & 3') for analysing for redundancy within a gene |
10 |
extatic |
singleseq=X |
Analyse a single sequence only (named X). cDNA and CDS should be sequence strings. |
None |
fiesta |
assmode=X |
Mode to use for EST assembly (nogab,gablam,oneqry) |
oneqry |
fiesta |
blastcut=X |
Reduced the number of sequences in HAQESAC runs to X (0 = no reduction) |
50 |
fiesta |
minaln=X |
Min length of shared region for consensus assembly |
40 |
fiesta |
minid=X |
Min identity of shared region for consensus assembly |
95.0 |
fiesta |
minorf=X |
Min length of ORFs to be considered |
20 |
fiesta |
minpolyat=X |
Min length of poly-AT to be considered a poly AT |
10 |
fiesta |
newacc=X |
New base for sequence accession numbers |
'' or spcode |
fiesta |
ntrim=X |
Trims of regions >= X proportion N bases |
0.5 |
fiesta |
qtype=X |
Sequence "Type" to be used with NewAcc for annotation of translations |
hit |
fiesta |
resave=X |
Number of ESTs to remove before each resave of GABLAM searchdb |
200 |
fiesta |
spcode=X |
Species code for EST sequences |
None |
fiesta |
species=X |
Species for EST sequences |
None |
file_monster |
dircut=X |
Max number of subdirectories to have and still delve into them |
50 |
file_monster |
dircut=X |
Max number of subdirectories to have and still delve into them |
50 |
file_monster |
dirdepth=X |
Max depth of subdirectories to delve into. Negative = all. |
-1 |
file_monster |
organise=X |
File reorganisation mode (none/date/month/compile) |
None |
file_monster |
orgprefix=X |
Prefix for organised outdir subdirectories |
'' |
file_monster |
prefix=X |
Text prefix for new file names |
|
file_monster |
searchid=X |
ID for search - allows multiple searches to be compared easily |
None |
file_monster |
searchid=X |
ID for search - allows multiple searches to be compared easily |
None |
file_monster |
sizematch=X |
Size % similarity threshold to count as match |
99.9 |
file_monster |
sortby=X |
Whether to sort by date or name |
date |
gablam |
addflanks=X |
Add flanking regions of length X to fragmented hits |
0 |
gablam |
alncut=X |
Perform ALIGN pairwise global alignment until < X %ID reached |
0 |
gablam |
blastb=X |
Number of hit alignments per query (BLAST -b X) |
500 |
gablam |
blaste=X |
E-Value cut-off for BLAST searches (BLAST -e X) |
1e-4 |
gablam |
blastp=X |
Type of BLAST search to perform (blastx for DNA vs prot; tblastn for Prot vs DNA) |
blastp |
gablam |
blastv=X |
Number of one-line hits per query (BLAST -v X) |
500 |
gablam |
bycluster=X |
Generate separate trees and distance matrix for clusters of X+ sequences |
0 |
gablam |
clustersplit=X |
Threshold at which clusters will be split (e.g. must be < distance to cluster) |
1.0 |
gablam |
cutfocus=X |
Focus for gablamcut. Can be Query/Hit/Either/Both. |
Either |
gablam |
cutstat=X |
Stat for gablamcut (eg. AlnLen or OrderedAlnSim. See Function docs for full list) |
OrderedAlnID |
gablam |
diskey=X |
GABLAM Output Key to be used for distance matrix |
'Qry_AlnID' |
gablam |
dotlocalmin=X |
Minimum length of local alignment to output to local hit dot plots |
1000 |
gablam |
evalaln=X |
Perform ALIGN pairwise global alignment for all hits with e <= X |
1000 |
gablam |
forks=X |
Number of parallel sequences to process at once |
0 |
gablam |
fragmerge=X |
Max Length of gaps between fragmented local hits to merge |
0 |
gablam |
gablamcut=X |
Min. percentage value for a GABLAM stat to report hit (GABLAM from FASTA only) |
0.0 |
gablam |
gablamfrag=X |
Length of gaps between mapped residues for fragmenting local hits |
0 |
gablam |
killforks=X |
Number of seconds of no activity before killing all remaining forks. |
36000 |
gablam |
localcut=X |
Cut-off length for local alignments contributing to global GABLAM stats |
0 |
gablam |
localmin=X |
Minimum length of local alignment to output to local stats table |
0 |
gablam |
localsort=X |
Local hit field used to sort local alignments for localunique reduction |
Identity |
gablam |
maxall=X |
Maximum number of sequences for all-by-all outputs |
100 |
gablam |
nrcut=X |
Cut-off for non-redundancy filter, uses nrstat=X for either query or hit |
100.0 |
gablam |
nrstat=X |
Stat for nrcut (eg. AlnLen or OrderedAlnSim. See above for full list) |
OrderedAlnID |
gablam |
outstats=X |
Whether to output just GABLAM, GABLAMO or All |
All |
gablam |
rankaln=X |
Perform ALIGN pairwise global alignment for top X hits |
0 |
gablam |
reftype=X |
Whether to map SAM/GFF3 hits onto the Qry, Hit, Both or Combined |
Hit |
gablam |
startfrom=X |
Accession number to start from |
None |
gatic |
flanks=X |
Length of flanks for profile analysis etc. |
20 |
gatic |
species=X |
Species for analysis |
HUMAN |
gfessa |
allreptag=X |
Filter out any Tags that are not returned by ALL replicates of X experiments |
0 |
gfessa |
basefile=X |
"Base" name for all results files, e.g. X.gfessa.tdt |
TAG file basename |
gfessa |
enrcut=X |
Minimum mean fold change between experiments |
2.5 |
gfessa |
minabstag=X |
Minimum individual number of counts for a tag to be included (ANY one replicate) |
5 |
gfessa |
minenrtag=X |
Minimum number of counts for a tag to be retained for enrichment etc. (summed replicates) |
15 |
gfessa |
minexptag=X |
Minimum number of experiments for a tag to be included (no. replicates) |
3 |
gfessa |
mintag=X |
Minimum total number of counts for a tag to be included (summed replicates) |
0 |
gfessa |
mismatch=X |
No. mismatches to allow. -1 = Exact matching w/o BLAST |
-1 |
gfessa |
normalise=X |
Method for normalising tag counts within replicate (None/ppm) |
ppm |
gfessa |
pwenr=X |
Minimum fold change between pairwise experiment comparisons |
1.0 |
gfessa |
tagfield=X |
Field in tagfile containing tag sequence. (All others should be counts) |
'Tag sequence' |
gfessa |
taglen=X |
Length of sequence tags |
26 |
gfessa |
tagstart=X |
Sequence starting tags |
'CATG' |
gopher |
alnprog=X |
Choice of alignment program to use (clustalw/clustalo/muscle/mafft/fsa) |
clustalo |
gopher |
gablamo=X |
GABLAMO measure to use for similarity measures |
Sim |
gopher |
maxpara=X |
Maximum number of paralogues to consider (large gene families can cause problems) |
50 |
gopher |
minsim=X |
Minimum %similarity of Query for each "orthologue" |
40.0 |
gopher |
orthid=X |
File identifier (Lower case) for orthology files |
orth |
gopher |
simfocus=X |
Style of similarity comparison used for MinSim and "Best" sequence identification |
query |
gopher |
startfrom=X |
Accession Number / ID to start from. (Enables restart after crash.) |
None |
gopher |
stiggid=X |
Base for Stigg ID numbers |
STIGG |
gopher_V2 |
gablamo=X |
GABLAMO measure to use for similarity measures |
Sim |
gopher_V2 |
maxpara=X |
Maximum number of paralogues to consider (large gene families can cause problems) |
50 |
gopher_V2 |
minsim=X |
Minimum %similarity of Query for each "orthologue" |
40.0 |
gopher_V2 |
simfocus=X |
Style of similarity comparison used for MinSim and "Best" sequence identification |
query |
gopher_V2 |
startfrom=X |
Accession Number / ID to start from. (Enables restart after crash.) |
None |
gopher_V2 |
stiggid=X |
Base for Stigg ID numbers |
STIGG |
happi |
border=X |
Border setting for tables |
0 |
happi |
classcol=X |
Table of "Class" and "Col" (soton$col indexes) to be used for PPI images |
basefile.col.tdt |
happi |
geneclass=X |
Field used to identify class of Genes |
'Class' |
happi |
genefield=X |
Field to be used for indentifying Genes |
'Gene' |
happi |
gopages=X |
Create Pages of GO terms with X+ representative genes |
5 |
happi |
infotext=X |
Text to display under header |
'This data has not yet been published and should not be used without permission.' |
happi |
maxgo=X |
Go terms above X genes will not have gene data tabs |
500 |
happi |
pagehead=X |
Text for Front Page Header |
'HAPPI Analysis of basefile' |
happi |
pngmax=X |
Max number of genes for PNG construction |
2000 |
happi |
ppexpand=X |
Expand PPI by X levels for MCODE complex generation |
1 |
haqesac |
acclist=X |
Extract only AccNums in list. X can be FILE or list of AccNums X,Y,.. |
None |
haqesac |
basefile=X |
Basic 'root' for all files X.* |
By default will use 'root' of seqin=FILE if given or haq_AccNum if qblast |
haqesac |
blastcut=X |
Maximum number of sequences to have in dataset (BLAST query against NR dataset.) |
0 |
haqesac |
blaste=X |
E-Value cut-off for BLAST searches (BLAST -e X) |
1e-4 |
haqesac |
blastv=X |
Number of one-line hits per query (BLAST -v X) |
500 |
haqesac |
cwcut=X |
Total number of residues above which to use ClustalW for alignment in place of alnprog=X |
0 |
haqesac |
d=X |
Data output level (0-3, see docstring) |
1 |
haqesac |
fam=X |
minimum number of families (If 0, no subfam grouping) |
0 |
haqesac |
fixpam=X |
PAM distance fixed to X |
0 |
haqesac |
groupspec=X |
Species for duplication grouping |
None |
haqesac |
i=X |
Sets interactivity (-1 for full auto) |
0 |
haqesac |
maketree=X |
Program for making tree |
None |
haqesac |
maxgap=X |
Maximum proportion of sequence that may be gaps compared to nearest neighbour (<=0 = No maximum) |
0.5 |
haqesac |
maxlen=X |
Maximum length of sequences (<=0 = No maximum) |
0 |
haqesac |
mfs=X |
minimum family size |
3 |
haqesac |
minlen=X |
Minimum length of sequences |
0 |
haqesac |
nrid=X |
%Identity cut-off for Non-Redundancy |
99.0 |
haqesac |
pairid=X |
Fasta Alignment ID cut-off for any pair of sequences |
0.0 |
haqesac |
pamcut=X |
Absolute maximum PAM matrix |
1000 |
haqesac |
pammax=X |
Initial maximum PAM matrix to generate |
100 |
haqesac |
paqb=X |
PAQ Block length. |
7 |
haqesac |
paqkl=X |
Relative Weighting of keeping Length in PAQ. |
1 |
haqesac |
paqks=X |
Relative Weighting of keeping Sequences in PAQ. |
3 |
haqesac |
paqm=X |
Min score in PAQ Block (Default matrix: No. residues to match). |
3 |
haqesac |
qcover=X |
Min. % (ordered) BLAST coverage of Query vs Hit or Hit vs Query |
60.0 |
haqesac |
qfastacmd=X |
Extract query X from qblast database using fastacmd (may also need query=X) |
None |
haqesac |
qryid=X |
Fasta Alignment ID with Query cut-off |
40.0 |
haqesac |
rarecut=X |
Rare aa cut-off |
0.05 |
haqesac |
saqb=X |
SAQ Block length. |
10 |
haqesac |
saqc=X |
Min score for a residue in SAQ (Default matrix: no. seqs to share residue). |
2 |
haqesac |
saqkl=X |
Relative Weighting of keeping Length in SAQ. |
1 |
haqesac |
saqks=X |
Relative Weighting of keeping Sequences in SAQ. |
3 |
haqesac |
saqm=X |
No. residues to match in SAQ Block. |
7 |
haqesac |
specdup=X |
Minimum number of different species in clade to be identified as a duplication |
2 |
haqesac |
v=X |
Sets verbosity (-1 for silent) |
0 |
haqesac |
xpass=X |
How many extra passes to make down & up tree after initial GASP |
1 |
humsf09 |
fdranncut=X |
FDR cut-off for manual annotation |
0.05 |
humsf10 |
sigcut=X |
Significance cut-off for analyses |
0.01 |
jrj_fastq |
maxbad=X |
Maximmum number of (internal) bases that can remain below qcut |
0 |
jrj_fastq |
meanqc=X |
Minimum mean QC to keep |
0.0 |
jrj_fastq |
minlen=X |
Minimum length of sequence that must remain after QC trimming |
0 |
jrj_fastq |
qcut=X |
Quality control cut-off. Trim residues below this QC threshold. |
20 |
jrj_fastq |
qprop=X |
Proportion of sequence that must remain after QC trimming |
0.8 |
multihaq |
blastcut=X |
Restrict HAQESAC and MultiHAQ BLAST searches to top X BLAST hits |
0 |
multihaq |
multicut=X |
Restrict MultiHAQ BLASTs to the top X hits from each database (over-rides blastcut) |
0 |
orcfinder |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
orcfinder |
homcut=X |
Max number of homologues to allow (to reduce large multi-domain families) |
200 |
orcfinder |
maxseq=X |
Maximum number of sequences to process |
500 |
orcfinder |
maxupc=X |
Maximum UPC size of dataset to process |
0 |
orcfinder |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
pagsat |
basefile=X |
Basename for output files and directories. |
assembly+ref |
pagsat |
joinmargin=X |
Number of extra bases allowed to still be considered an end local BLAST hit |
10 |
pagsat |
joinmerge=X |
Merging mode for joining chromosomes (mid/start/end/longest) |
mid |
pagsat |
joinsort=X |
Whether to sort potential chromosome joins by `Length` or `Identity` |
Identity |
pagsat |
mincontiglen=X |
Minimum contig length to retain in assembly (QV filtering only) |
1000 |
pagsat |
minlocid=X |
Minimum percentage identity for local hits mapping to chromosome coverage |
95.0 |
pagsat |
minloclen=X |
Mininum length for local hits mapping to chromosome coverage |
250 |
pagsat |
minqv=X |
Minimum mean QV score for assembly contigs (read from *.qv.csv) |
20 |
pagsat |
minunique=X |
Minimum number of "Unique-mapping" nucleotides to retain a contig-chromosome link |
250 |
pagsat |
newacc=X |
New base for edited contig accession numbers (None will keep old accnum) |
None |
pagsat |
newchr=X |
Code to replace "chr" in new sequence names for additional PAGSAT compatibility |
ctg |
pagsat |
refchr=X |
Code used in place of "chr" for reference sequence names |
chr |
pagsat |
spcode=X |
Species code for reference genome (if not already processed by rje_genbank) |
None |
pagsat |
tophitbuffer=X |
Percentage identity difference to keep best hits for reference genes/proteins. |
1.0 |
pagsat_V1 |
basefile=X |
Basename for output files and directories. |
assembly+ref |
pagsat_V1 |
chrmap=X |
Contig:Chromosome mapping mode for assembly tidy (unique/align) |
unique |
pagsat_V1 |
joinmargin=X |
Number of extra bases allowed to still be considered an end local BLAST hit |
10 |
pagsat_V1 |
joinmerge=X |
Merging mode for joining chromosomes (consensus/end) |
end |
pagsat_V1 |
joinsort=X |
Whether to sort potential chromosome joins by `Length` or `Identity` |
Identity |
pagsat_V1 |
mincontiglen=X |
Minimum contig length to retain in assembly (QV filtering only) |
1000 |
pagsat_V1 |
minlocid=X |
Minimum percentage identity for local hits mapping to chromosome coverage |
95.0 |
pagsat_V1 |
minloclen=X |
Mininum length for local hits mapping to chromosome coverage |
250 |
pagsat_V1 |
minqv=X |
Minimum mean QV score for assembly contigs (read from *.qv.csv) |
20 |
pagsat_V1 |
newacc=X |
New base for edited contig accession numbers (None will keep old accnum) |
None |
pagsat_V1 |
newchr=X |
Code to replace "chr" in new sequence names for additional PAGSAT compatibility |
ctg |
pagsat_V1 |
spcode=X |
Species code for reference genome (if not already processed by rje_genbank) |
None |
pagsat_V1 |
tophitbuffer=X |
Percentage identity difference to keep best hits for reference genes/proteins. |
1.0 |
patis |
basefile=X |
Leader for *.utr5.fas and *.cds.fas sequences - should start with species |
Homo_sapiens.GRCh37.p13 |
patis |
blaste=X |
E-value cut-off for BLAST search |
1e-10 |
patis |
forks=X |
Number of forks for GABLAM run |
0 |
patis |
gablamcut=X |
Percentage identity cut-off for mapping to clones |
95.0 |
patis |
minfrag=X |
Minimum length of fragment to clone |
303 |
patis |
minorf=X |
Min length of extended ORF |
20 |
patis |
orthbase=X |
Basefile for AIC prediction on orthologous species |
Mus_musculus.NCBIM37.64 |
patis |
orthspec=X |
Species in which to look for conservation etc. of orthologues |
Mouse |
patis |
ratings=X |
Which rating scheme to use for AIC (biol2013/jan14) |
'jan14' |
peptcluster |
maxgapvar=X |
Maximum number of consecutive gaps to allow for peptide alignment without Regex guide |
3 |
peptcluster |
maxgapx=X |
Maximum total number of gaps to allow for peptide alignment without Regex guide |
5 |
peptcluster |
outmatrix=X |
Type for output matrix - tdt / csv / mysql / phylip / png |
tdt |
peptcluster |
peptalign=T/F/X |
Align peptides. Will use as guide regular expression, else T/True for regex-free alignment. |
|
peptcluster |
peptcluster=X |
Clustering mode (upgma/wpgma/neighbor) |
upgma |
peptcluster |
peptdis=X |
Method for generating pairwise peptide distances (id/prop/pam) |
prop |
peptide_dismatrix |
method=X |
Peptide Distance Method to use |
ds_prop |
peptide_dismatrix |
outmatrix=X |
Type for output matrix - text / mysql / phylip |
Phylip |
pic_html |
fontface=X |
Font to use for text |
Comic Sans MS |
pic_html |
hometitle="X" |
Title to use for home web page |
"Photo Page" |
pic_html |
picfolder=X |
Name of primary folder to look in for photos |
* |
pic_html |
thumbheight=X |
Height of thumbnails (pixels) in Preview pages |
120 |
pic_html |
thumbnails=X |
Folder containing thumbnails for all pictures of this type |
thumbnails |
pic_html |
thumbname=X |
Name to distinguish thumbnails from actual pictures (will rename) |
_thumb |
picsi |
delimit=X |
Delimiter for output files |
tab |
pingu_V3 |
allbyall=X |
Generates an all-by-all table of PPI links upto X degrees of separation (sample only) |
0 |
pingu_V3 |
basefile=X |
Results file prefix if no data file given with data=FILE |
pingu |
pingu_V3 |
combaits=X |
Whether to combine bait PPIs into single sample (X) (if addbaits=T) |
|
pingu_V3 |
fasid=X |
Text ID for PPI fasta files |
'ppi' |
pingu_V3 |
makefam=X |
GABLAM Percentage identity threshold for grouping sequences into families |
0.0 |
pingu_V3 |
pathfinder=X |
Perform (lengthy) PathFinder analysis to link genes upto X degree separation (-1 = no limit) |
0 |
pingu_V3 |
randnum=X |
Number of randomisations |
1000 |
pingu_V3 |
randseed=X |
Seed for randomiser |
0 |
pingu_V3 |
remsticky=X |
Remove "sticky" hubs as defined by >X known PPI |
0 |
pingu_V3 |
xgexpand=X |
Expand XGMML network with additional levels of interactors |
0 |
pingu_V4 |
basefile=X |
Results file prefix |
pingu |
pingu_V4 |
fasid=X |
Text ID for fasta files (*.X.fas) |
default named after ppisource(+'-dom') |
pingu_V4 |
minppi=X |
Minimum number of PPI for file output |
0 |
pingu_V4 |
ppisource=X |
Source of PPI data. (HINT/FILE) FILE needs 'Hub', 'Spoke' and 'SpokeUni' fields. |
'HINT' |
pingu_V4 |
unifield=X |
Uniprot accession number field identifier for xrefdata |
'Uniprot' |
presto_V5 |
alnext=X |
File extension of alignment files, accnum.X |
aln.fas |
presto_V5 |
ambcut=X |
Cut-off for max number of choices in ambiguous position to be shown as variant |
10 |
presto_V5 |
conscore=X |
Type of conservation score used: |
pos |
presto_V5 |
consweight=X |
Weight given to global percentage identity for conservation, given more weight to closer sequences |
0 |
presto_V5 |
expcut=X |
The maximum number of expected occurrences allowed to still search with motif |
0 |
presto_V5 |
flanksize=X |
Size of sequence flanks for motifs |
30 |
presto_V5 |
hitname=X |
Format for Hit Name: full/short/accnum |
short |
presto_V5 |
iucut=X |
Cut-off for IUPred results (0.0 will report mean IUPred score) |
0.0 |
presto_V5 |
iumethod=X |
IUPred method to use (long/short) |
short |
presto_V5 |
matchfix=X |
If >0 must exactly match *all* fixed positions in the motifs from: |
0 |
presto_V5 |
minfix=X |
Min number of fixed positions for a motif to contain |
0 |
presto_V5 |
minic=X |
Min information content for a motif (1 fixed position = 1.0) |
2.0 |
presto_V5 |
minpep=X |
Min length of motif/peptide X aa |
2 |
presto_V5 |
minshare=X |
Min. number of non-wildcard positions for motifs to share |
2 |
presto_V5 |
motdesc=X |
Sets which motifs have description outputs (0-3 as matchfix option) |
3 |
presto_V5 |
outfile=X |
Base name of results files, e.g. X.presto.tdt. |
motifsFILE-searchdbFILE.presto.tdt |
presto_V5 |
outstyle=X |
Sets the output style for the resfile |
normal |
presto_V5 |
runid=X |
Adds an additional Run_ID column identifying the run (for multiple appended runs |
None |
presto_V5 |
startfrom=X |
Accession Number / ID to start from. (Enables restart after crash.) |
None |
presto_V5 |
winchg=X |
Extend charge calculations (if any) to X aa either side of motif |
0 |
presto_V5 |
windis=X |
Extend disorder statistic X aa either side of motif (use flanks *only* if negative) |
0 |
presto_V5 |
winhyd=X |
Number of aa to extend Eisenberg Hydrophobicity calculation either side of motif |
0 |
presto_V5 |
winsa=X |
Number of aa to extend Surface Accessibility calculation either side of motif |
0 |
presto_V5 |
winsize=X |
Sets all of the above window sizes (use flanks *only* if negative) |
0 |
presto_V5 |
xdivide=X |
Size of dividing Xs between motifs |
10 |
presto_V5 |
xpad=X |
Adds X additional Xs to the flanks of the motif (after trimx if trimx=T) |
0 |
presto_V5 |
xpaddb=X |
Adds X additional Xs to the flanks of the search database sequences (will mess up alignments) |
0 |
prodigis |
maxpeplen=X |
Maximum peptide length to individually return |
40 |
prodigis |
minpeplen=X |
Minimum peptide length to consider |
0 |
prodigis |
pepcut=X |
Protease used to generate list of identified peptides |
tryp |
prothunter |
basefile=X |
This will control output file names and also be used to pick up later analyses for HTML etc. |
|
qslimfinder |
absmin=X |
Used if minocc<1 to define absolute min. UP occ |
3 |
qslimfinder |
absminamb=X |
Used if ambocc<1 to define absolute min. UP occ |
2 |
qslimfinder |
ambocc=X |
Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) |
0.05 |
qslimfinder |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
qslimfinder |
casemask=X |
Mask Upper or Lower case |
None |
qslimfinder |
clouds=X |
Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) |
2 |
qslimfinder |
extras=X |
Whether to generate additional output files (alignments etc.) |
1 |
qslimfinder |
focusocc=X |
Motif must appear in X+ focus groups (0 = all) |
0 |
qslimfinder |
homcut=X |
Max number of homologues to allow (to reduce large multi-domain families) |
0 |
qslimfinder |
maxseq=X |
Maximum number of sequences to process |
500 |
qslimfinder |
maxupc=X |
Maximum UPC size of dataset to process |
0 |
qslimfinder |
maxwild=X |
Maximum number of consecutive wildcard positions to allow |
2 |
qslimfinder |
minic=X |
Minimum information content for returned motifs |
2.1 |
qslimfinder |
minocc=X |
Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) |
0.05 |
qslimfinder |
minwild=X |
Minimum number of consecutive wildcard positions to allow |
0 |
qslimfinder |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
qslimfinder |
probcut=X |
Probability cut-off for returned motifs |
0.1 |
qslimfinder |
probscore=X |
Score to be used for probability cut-off and ranking (Prob/Sig) |
Sig |
qslimfinder |
runid=X |
Run ID for resfile (allows multiple runs on same data) |
DATE:TIME |
qslimfinder |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
qslimfinder |
sizesort=X |
Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) |
0 |
qslimfinder |
slimlen=X |
Maximum length of SLiMs to return (no. non-wildcard positions) |
5 |
qslimfinder |
topranks=X |
Will only output top X motifs meeting probcut |
1000 |
qslimfinder |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
qslimfinder_V1.9 |
absmin=X |
Used if minocc<1 to define absolute min. UP occ |
3 |
qslimfinder_V1.9 |
absminamb=X |
Used if ambocc<1 to define absolute min. UP occ |
2 |
qslimfinder_V1.9 |
ambocc=X |
Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) |
0.05 |
qslimfinder_V1.9 |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
qslimfinder_V1.9 |
casemask=X |
Mask Upper or Lower case |
None |
qslimfinder_V1.9 |
clouds=X |
Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) |
2 |
qslimfinder_V1.9 |
extras=X |
Whether to generate additional output files (alignments etc.) |
1 |
qslimfinder_V1.9 |
focusocc=X |
Motif must appear in X+ focus groups (0 = all) |
0 |
qslimfinder_V1.9 |
homcut=X |
Max number of homologues to allow (to reduce large multi-domain families) |
0 |
qslimfinder_V1.9 |
maxseq=X |
Maximum number of sequences to process |
500 |
qslimfinder_V1.9 |
maxupc=X |
Maximum UPC size of dataset to process |
0 |
qslimfinder_V1.9 |
maxwild=X |
Maximum number of consecutive wildcard positions to allow |
2 |
qslimfinder_V1.9 |
minic=X |
Minimum information content for returned motifs |
2.1 |
qslimfinder_V1.9 |
minocc=X |
Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) |
0.05 |
qslimfinder_V1.9 |
minwild=X |
Minimum number of consecutive wildcard positions to allow |
0 |
qslimfinder_V1.9 |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
qslimfinder_V1.9 |
probcut=X |
Probability cut-off for returned motifs |
0.1 |
qslimfinder_V1.9 |
probscore=X |
Score to be used for probability cut-off and ranking (Prob/Sig) |
Sig |
qslimfinder_V1.9 |
runid=X |
Run ID for resfile (allows multiple runs on same data) |
DATE:TIME |
qslimfinder_V1.9 |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
qslimfinder_V1.9 |
sizesort=X |
Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) |
0 |
qslimfinder_V1.9 |
slimlen=X |
Maximum length of SLiMs to return (no. non-wildcard positions) |
5 |
qslimfinder_V1.9 |
topranks=X |
Will only output top X motifs meeting probcut |
1000 |
qslimfinder_V1.9 |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
revert |
blaste=X |
BLAST evalue cut-off |
1e-10 |
revert |
farmgablam=X |
Whether to run a pre-REVERT farming of batch BLAST searches using X forks each |
0 |
revert |
gablamfrag=X |
Length of gaps between mapped residues for fragmenting local hits |
100 |
revert |
minpcov=X |
Min. %coverage for viral proteins during NR reduction |
40.0 |
revert |
minplocid=X |
Min. local %identity for viral proteins during NR reduction |
30.0 |
revert |
minvcov=X |
Min. %coverage for viral genomes during NR reduction |
40.0 |
revert |
minvlocid=X |
Min. local %identity for viral genomes during NR reduction |
30.0 |
rje |
delimit=X |
Sets standard delimiter for results output files |
\t |
rje |
forks=X |
Number of parallel sequences to process at once |
0 |
rje |
i=X |
Sets interactivity (-1 for full auto) |
0 |
rje |
killforks=X |
Number of seconds of no activity before killing all remaining forks. |
36000 |
rje |
maxbin=X |
Maximum number of trials for using binomial (else use Poisson) |
- |
rje |
rest=X |
Variable that sets the output to be returned by REST services |
None |
rje |
v=X |
Sets verbosity (-1 for silent) |
0 |
rje_1433 |
sqcut=X |
Sequest score cutoff. Scores must be greater than or equal to this |
0.95 |
rje_1433 |
xtcap=X |
XTandem score cap ("Best" X-Tandem score) |
-10 |
rje_1433 |
xtcut=X |
XTandem score cutoff. Scores must be less than or equal to this |
-2.5 |
rje_aaprop |
aagapdif=X |
Property difference given to amino acid vs gap comparisons |
5 |
rje_aaprop |
aanulldif=X |
Property difference given to amino acid vs null values (e.g. X) |
0.5 |
rje_aic |
flank=X |
Length for 5' flanking sequence |
1000 |
rje_aic |
kozak=X |
Basename for Kozak analysis input |
'Homo_sapiens.GRCh37.56' |
rje_aic |
kozwin=X |
No. of nucleotides either side of start codon |
21 |
rje_aic |
nrgene=X |
Which gene type to use for redundancy removal (Gene/EnsG) |
'Gene' |
rje_aic |
rep=X |
Number of random replicates |
1000 |
rje_aic |
shortutr=X |
5' UTR
10 |
|
rje_ancseq |
fixpam=X\t |
PAM distance fixed to X |
0 |
rje_ancseq |
rarecut=X\t |
Rare aa cut-off |
0.05 |
rje_ancseq |
xpass=X\t |
How many extra passes to make down & up tree after initial GASP |
1 |
rje_archive |
dormancy=X |
Min number of days of inactivity before a directory gets rated as dormant (0=no dormancy) |
30 |
rje_archive |
quiet=X |
Min number of days of inactivity before a directory gets rates as quiet |
1 |
rje_archive |
rds=X |
UNSW_RDS project code to use (e.g. D0234444) |
|
rje_archive |
uploadsh=X |
Full path for runnining upload.sh script |
'/share/apps/unswdataarchive/2015-09-10/upload.sh' |
rje_biogrid |
dbsource=X |
Source database (biogrid/dip/intact/mint/reactome) |
biogrid |
rje_biogrid |
minseq=X |
Minimum number of PPI sequences in order to output fasta file |
3 |
rje_biogrid |
species=X |
Name of species to use data for (will be read from file if BioGRID) |
human |
rje_blast |
blasta=X |
Number of processors to use (BLAST -a X) |
1 |
rje_blast |
blastb=X |
Number of hit alignments per query (BLAST -b X) |
250 |
rje_blast |
blaste=X |
E-Value cut-off for BLAST searches (BLAST -e X) |
1e-4 |
rje_blast |
blastp=X |
BLAST program (BLAST -p X) |
blastp |
rje_blast |
blastpath=X |
path for blast files |
c:/bioware/blast/ |
rje_blast |
blastv=X |
Number of one-line hits per query (BLAST -v X) |
500 |
rje_blast |
gablamfrag=X |
Length of gaps between mapped residue for fragmenting local hits |
100 |
rje_blast |
localcut=X |
Cut-off length for local alignments contributing to global GABLAM stats) |
0 |
rje_blast_V1 |
blasta=X |
Number of processors to use (BLAST -a X) |
1 |
rje_blast_V1 |
blastb=X |
Number of hit alignments per query (BLAST -b X) |
250 |
rje_blast_V1 |
blaste=X |
E-Value cut-off for BLAST searches (BLAST -e X) |
1e-4 |
rje_blast_V1 |
blastp=X |
BLAST program (BLAST -p X) |
blastp |
rje_blast_V1 |
blastpath=X |
path for blast files |
'' |
rje_blast_V1 |
blastv=X |
Number of one-line hits per query (BLAST -v X) |
500 |
rje_blast_V1 |
gablamfrag=X |
Length of gaps between mapped residue for fragmenting local hits |
100 |
rje_blast_V1 |
localcut=X |
Cut-off length for local alignments contributing to global GABLAM stats) |
0 |
rje_blast_V2 |
blasta=X |
Number of processors to use (BLAST -a X) |
1 |
rje_blast_V2 |
blastb=X |
Number of hit alignments per query (BLAST -b X) |
500 |
rje_blast_V2 |
blaste=X |
E-Value cut-off for BLAST searches (BLAST -e X) |
1e-4 |
rje_blast_V2 |
blastprog=X |
BLAST program to use. blastp=X also recognised. (BLAST -p X) |
blastp |
rje_blast_V2 |
blastv=X |
Number of one-line hits per query (BLAST -v X) |
500 |
rje_blast_V2 |
fragmerge=X |
Max Length of gaps between fragmented local hits to merge |
0 |
rje_blast_V2 |
gablamfrag=X |
Length of gaps between mapped residue for fragmenting local hits |
100 |
rje_blast_V2 |
localcut=X |
Cut-off length for local alignments contributing to global GABLAM stats) |
0 |
rje_blast_V2 |
qconsensus=X |
Whether to convert QAssemble alignments to consensus sequences (None/Hit/Full) |
None |
rje_blast_V2 |
reftype=X |
Whether to map SAM/GFF3 hits onto the Qry, Hit, Both or Combined |
Hit |
rje_blast_V2 |
tophits=X |
Sets max number of BLAST hits returned (blastb and blastv) |
500 |
rje_chlamydia |
winsize=X |
Window size for NT composition plots |
5000 |
rje_chlamydia |
winstep=X |
Window step size for NT composition plots |
1000 |
rje_disorder |
disorder=X |
Disorder method to use (iupred/foldindex/anchor/parse) |
iupred |
rje_disorder |
filoop=X |
Number of times to try connecting to FoldIndex server |
10 |
rje_disorder |
fisleep=X |
Number of seconds to sleep between attempts |
2 |
rje_disorder |
iucut=X |
Cut-off for IUPred/ANCHOR results |
0.2 |
rje_disorder |
iumethod=X |
IUPred method to use (long/short) |
short |
rje_disorder |
minregion=X |
Minimum length of an ordered/disordered region |
0 |
rje_disorder |
name=X |
Name of sequence to predict disorder for |
|
rje_disorder |
sequence=X |
Sequence to predict disorder for (autorun) |
|
rje_embl |
lcft=X |
Feature to add for LowerCase portions of sequence |
|
rje_embl |
outformat=X |
Format for generated DAT file (uniprot/embl) |
embl |
rje_embl |
ucft=X |
Feature to add for UpperCase portions of sequence |
|
rje_ensembl |
automap=X |
Minimum value of mapstat for mapping to occur |
80.0 |
rje_ensembl |
mapstat=X |
GABLAM Stat to use for mapping assessment (ID/Sim/Len) |
ID |
rje_ensembl |
mingo=X |
Minumum number of genes to output GO category |
0 |
rje_ensembl |
resume=X |
Species or species code to pickup run from |
None |
rje_ensembl |
specsleep=X |
Sleep for X seconds between species downloads |
60 |
rje_forker |
forks=X |
Number of parallel sequences to process at once |
0 |
rje_forker |
forksleep=X |
Sleep time (seconds) between cycles of forking out more process |
0 |
rje_forker |
iolimit=X |
Limit of number of IOErrors before termination |
50 |
rje_forker |
killforks=X |
Number of seconds of no activity before killing all remaining forks. |
36000 |
rje_forker |
memfree=X |
Min. proportion of node memory to be free before spawning new fork |
0.1 |
rje_genbank |
geneacc=X |
Feature detail to use for gene sequence accession number (added to details) |
locus_tag |
rje_genbank |
protacc=X |
Feature detail to use for protein sequence accession number (added to details) |
protein_id |
rje_genbank |
spcode=X |
Overwrite species read from file (if any!) with X |
None |
rje_genecards |
species=X |
Species to output in table |
Human |
rje_genemap |
basefile=X |
Root for output files |
genemap |
rje_genemap |
keyid=X |
Key field header to be used in main Data dictionary - aliases map to this |
Symbol |
rje_genomics |
begfield=X |
Field for beginning position |
QryStart |
rje_genomics |
endfield=X |
Field for end position |
HitStart |
rje_genomics |
queryfield=X |
Field defining the Query ("Read") name |
Qry |
rje_genomics |
reformat=X |
Output format (GFF3/SAM) |
GFF3 |
rje_genomics |
targetfield=X |
Field defining the Target (Genome contig) name |
Hit |
rje_glossary |
copyright=X |
Copyright statement for page |
'RJ Edwards 2012' |
rje_glossary |
htmlstyle=X |
Output HTML style for splits (tab/table/h3) |
h3 |
rje_glossary |
name=X |
Title for HTML output |
'Glossary' |
rje_glossary |
splits=X |
Number of sets to divide terms into |
6 |
rje_glossary |
termsplit=X |
Text to use for splitting term from description (if file extension not recognised) |
tab |
rje_haq |
paqb=X |
PAQ Block length. |
7 |
rje_haq |
paqkl=X |
Relative Weighting of keeping Length in PAQ. |
1 |
rje_haq |
paqks=X |
Relative Weighting of keeping Sequences in PAQ. |
3 |
rje_haq |
paqm=X |
No. residues to match in PAQ Block. |
3 |
rje_haq |
saqb=X |
SAQ Block length. |
10 |
rje_haq |
saqc=X |
Min no. seqs to share residue in SAQ. |
2 |
rje_haq |
saqkl=X |
Relative Weighting of keeping Length in SAQ. |
1 |
rje_haq |
saqks=X |
Relative Weighting of keeping Sequences in SAQ. |
3 |
rje_haq |
saqm=X |
No. residues to match in SAQ Block. |
7 |
rje_hm_html |
border=X |
Border setting for tables |
0 |
rje_hpc |
basefile=X |
Base for output files - compiled from individual run results |
None |
rje_hpc |
farm=X |
Program to farm out using seqbyseq mode. |
|
rje_hpc |
hpcmode=X |
Mode to be used for farming jobs between nodes (rsh/fork) |
fork |
rje_hpc |
iolimit=X |
Limit of number of IOErrors before termination |
50 |
rje_hpc |
keepfree=X |
Number of processors to keep free on head node |
1 |
rje_hpc |
memfree=X |
Min. proportion of node memory to be free before spawning job |
0.0 |
rje_hpc |
pickhead=X |
Header to extract from OutList file and used to populate AccNum to skip |
|
rje_hpc |
startfrom=X |
Sequence ID at which to begin the SeqBySeq farming |
None |
rje_hpc |
subsleep=X |
Sleep time (seconds) between cycles of subbing out jobs to hosts |
1 |
rje_html |
analytics=X |
Google Analytics code to use with pages |
|
rje_html |
border=X |
Border setting for tables |
0 |
rje_html |
copyright=X |
Copyright statement for page |
'RJ Edwards 2015' |
rje_html |
title=X |
Default title for HTML page |
|
rje_iridis |
basefile=X |
Base for output files - compiled from individual run results |
None |
rje_iridis |
iolimit=X |
Limit of number of IOErrors before termination |
50 |
rje_iridis |
irun=X |
Exectute a special iRun analysis on Iridis (gopher/slimfinder/qslimfinder/slimsearch/unifake) |
|
rje_iridis |
keepfree=X |
Number of processors to keep free on head node |
1 |
rje_iridis |
memfree=X |
Min. proportion of node memory to be free before spawning job |
0.0 |
rje_iridis |
pickup=X |
Header to extract from OutList file and used to populate AccNum to skip |
|
rje_iridis |
pickup=X |
Header to extract from OutList file and used to populate AccNum to skip |
|
rje_iridis |
runid=X |
Text identifier for iX run |
None |
rje_iridis |
subsleep=X |
Sleep time (seconds) between cycles of subbing out jobs to hosts |
1 |
rje_itunes |
mintracks=X |
Min. number of tracks for averages |
1 |
rje_itunes |
toplist=X |
Number of entries to feature in HTML top lists |
20 |
rje_markov |
direction=X |
Direction to read chains (fwd/bwd/both) |
fwd |
rje_markov |
negvpos=X |
Perform Negatives versus Positives analysis on X.* files |
None |
rje_mirna |
maxseq=X |
Maximum number of sequences to process |
500 |
rje_mirna |
minmax=X |
Minimum value for Maximum expression value |
1.0 |
rje_misc |
job=X |
Identifier for the job to be performed |
None |
rje_mitab |
dbsource=X |
Source database for evidence field |
'mitab' |
rje_mitab |
unifield=X |
Uniprot accession number field identifier for xrefdata |
'Uniprot' |
rje_motif_V3 |
ambcut=X |
Cut-off for max number of choices in ambiguous position to be shown as variant (0=All) |
10 |
rje_motiflist |
alnext=X |
File extension of alignment files, accnum.X |
aln.fas |
rje_motiflist |
ambcut=X |
Cut-off for max number of choices in ambiguous position to be shown as variant |
10 |
rje_motiflist |
conscore=X |
Type of conservation score used: |
pos |
rje_motiflist |
consweight=X |
Weight given to global percentage identity for conservation, given more weight to closer sequences |
0 |
rje_motiflist |
flanksize=X |
Size of sequence flanks for motifs |
30 |
rje_motiflist |
iucut=X |
Cut-off for IUPred results (0.0 will report mean IUPred score) |
0.0 |
rje_motiflist |
iumethod=X |
IUPred method to use (long/short) |
short |
rje_motiflist |
minfix=X |
Min number of fixed positions for a motif to contain |
0 |
rje_motiflist |
minic=X |
Min information content for a motif (1 fixed position = 1.0) |
2.0 |
rje_motiflist |
minpep=X |
Min length of motif/peptide X aa |
2 |
rje_motiflist |
percentile=X |
Percentile steps to return in addition to mean |
0 |
rje_motiflist |
winchg=X |
Extend charge calculations (if any) to X aa either side of motif |
0 |
rje_motiflist |
windis=X |
Extend disorder statistic X aa either side of motif (use flanks *only* if negative) |
0 |
rje_motiflist |
winhyd=X |
Number of aa to extend Eisenberg Hydrophobicity calculation either side of motif |
0 |
rje_motiflist |
winsa=X |
Number of aa to extend Surface Accessibility calculation either side of motif |
0 |
rje_motiflist |
winsize=X |
Sets all of the above window sizes (use flanks *only* if negative) |
0 |
rje_motiflist |
xdivide=X |
Size of dividing Xs between motifs |
10 |
rje_obj |
delimit=X |
Sets standard delimiter for results output files |
\t |
rje_obj |
forks=X |
Number of parallel sequences to process at once |
0 |
rje_obj |
i=X |
Sets interactivity (-1 for full auto) |
0 |
rje_obj |
killforks=X |
Number of seconds of no activity before killing all remaining forks. |
36000 |
rje_obj |
maxbin=X |
Maximum number of trials for using binomial (else use Poisson) |
- |
rje_obj |
rest=X |
Variable that sets the output to be returned by REST services |
None |
rje_obj |
screenwrap=X |
Maximum width for some screen outputs |
200 |
rje_obj |
v=X |
Sets verbosity (-1 for silent, 0 for no progress counters) |
1 |
rje_pacbio |
avread=X |
Average read length (bp) |
20000 |
rje_pacbio |
errperbase=X |
Error-rate per base |
0.14 |
rje_pacbio |
genomesize=X |
Genome size (bp) |
0 |
rje_pacbio |
mapefficiency=X |
[Adv.] Efficiency of mapping anchor subreads onto seed reads for correction |
1.0 |
rje_pacbio |
maxcov=X |
Maximmum X coverage to calculate |
100 |
rje_pacbio |
minanchorx=X |
Minimum X coverage for anchor subreads |
6 |
rje_pacbio |
rqstep=X |
Size of RQ jumps for calculation (min 0.001) |
0.01 |
rje_pacbio |
smrtreads=X |
Average assemble output of a SMRT cell |
50000 |
rje_pacbio |
smrtunits=X |
Units for smrtreads=X (reads/Gb/Mb) |
reads |
rje_pacbio |
targetcov=X |
Target percentage coverage for final genome |
99.999 |
rje_pacbio |
targeterr=X |
Target errors per base for preassembly |
1/genome size |
rje_pacbio |
targetxcov=X |
Target 100% X Coverage for pre-assembly |
3 |
rje_pacbio |
xmargin=X |
"Safety margin" inflation of X coverage |
1 |
rje_pacbio |
xsteplen=X |
[Adv.] Size (bp) of increasing coverage steps for calculating required depths of coverage |
1e6 |
rje_pam |
pamcut=X |
Absolute maximum PAM matrix |
1000 |
rje_pam |
pamfile=X |
Sets PAM1 input file |
jones.pam |
rje_pam |
pammax=X |
Initial maximum PAM matrix to generate |
100 |
rje_paml |
basefile=X |
Base for names of results files |
'pamlres' |
rje_paml |
stripgap=X |
Strip codons with gaps in at least X sequences |
2 |
rje_pattern_discovery |
delimit=X |
Text delimiter |
\\t |
rje_pattern_discovery |
igap=X |
Information Content "Gap penalty" (wildcard penalisation) |
0 |
rje_pattern_discovery |
maxsup=X |
Max. number of sequences to have in file |
0 |
rje_pattern_discovery |
minsup=X |
Min. number of sequences to have in file |
3 |
rje_pattern_discovery |
remhub=X |
If X > 0.0, removes "hub" protien ("HUB_PPI") and any proteins >=X% identity to hub |
0.0 |
rje_pattern_discovery |
slimcall="X" |
Call for SLiMDisc in batch mode. May have leading commands. |
"python slimdisc_V1.4.py" |
rje_pattern_discovery |
slimopt="X" |
Text string of additional SLiMDisc options |
"" |
rje_pattern_discovery |
slimranks=X |
Return top X SLiMDisc ranked sequences |
1000 |
rje_pattern_discovery |
slimsupport=X |
Min. SLiMDisc support (-S X). If < 1, it is a proportion of input dataset size. |
0.1 |
rje_pattern_discovery |
slimversion=X |
Version of SLiMDisc to run (See slimcall=X for batch file jobs) |
1.4 |
rje_pattern_discovery |
slimwall=X |
TEIRESIAS walltime (minutes) in SLiMDisc run (-W X) |
60 |
rje_phos |
homsim=X |
Percentage identity (GABLAM; phosblast qry) for marking as homologue |
40.0 |
rje_phos |
idsim=X |
Percentage identity (GABLAM; phosblast qry) for marking as identity |
95.0 |
rje_ppi |
damping=X |
Force Directed Layout, damping parameter |
0.9 |
rje_ppi |
expandppi=X |
Expand reduced Node list by X PPI levels |
0 |
rje_ppi |
fluff=X |
MCODE "fluff" threshold. <0 = No Fluff |
0.5 |
rje_ppi |
fragsize=X |
Combine smaller fragments upto fragsize |
200 |
rje_ppi |
layout=X |
Layout to be used for XGMML output |
spring |
rje_ppi |
mindeg=X |
MCODE min degree for node scoring |
2 |
rje_ppi |
minfrag=X |
Minimum fragment size to keep |
3 |
rje_ppi |
mink=X |
MCODE min k-core values |
2 |
rje_ppi |
nodemap=X |
Try to map Nodes first using Node table field X |
|
rje_ppi |
nudgecyc=X |
Number of cycles between node nudges (try to bump out of unstable equilibria) |
1000 |
rje_ppi |
vwp=X |
MCODE vertex weighting percentage |
0.2 |
rje_ppi |
walltime=X |
Walltime (hours) for layouts |
0.02 |
rje_price |
fitness=X |
Fitness measurement |
cons |
rje_price |
normfit=X |
Normalise fitness to have mean of 1 |
False |
rje_price |
phenotype=X |
Phenotype measurement |
cons |
rje_price |
query=X |
Identifier of query sequence |
None |
rje_price |
seqgroup=X |
Sequence grouping method |
triplets |
rje_price |
special=X |
Instigate special run, e.g. allbyall |
None |
rje_pydocs |
author=X |
Author name to put at bottom of webpages |
RJ Edwards |
rje_pydocs |
email=X |
E-Mail address for general contact |
seqsuite@gmail.com |
rje_pydocs |
methodcap=X |
Maximum number of method calls before collapsed to single line |
0 |
rje_pydocs |
name=X |
Name for PyDoc run. Used for file naming and within documentation files. |
'pydocs' |
rje_pydocs |
release=X |
Release for packages |
YYYY-MM-DD |
rje_qsub |
dependhpc=X |
Name of HPC system for depend |
'blue30.iridis.soton.ac.uk' |
rje_qsub |
email=X |
Email address to email job stats to at end |
'' |
rje_qsub |
hpc=X |
Name of HPC system for depend |
'IRIDIS4' |
rje_qsub |
job=X |
Name of job file (.job added) |
qsub |
rje_qsub |
nodes=X |
Number of nodes to run on |
4 |
rje_qsub |
pause=X |
Wait X seconds before attempting showstart |
5 |
rje_qsub |
ppn=X |
Processors per node |
12 |
rje_qsub |
program=X |
Program call for Qsub (and options) |
None |
rje_qsub |
vmem=X |
Virtual Memory limit for run (GB) |
48 |
rje_qsub |
walltime=X |
Walltime for qsub job (hours) |
60 |
rje_samtools |
absmincut=X |
Absolute minimum read count for minor allele (used if mincut<1) |
2 |
rje_samtools |
basefile=X |
Basename for frequency comparison output |
.v. |
rje_samtools |
depthsmooth=X |
Smooth out any read plateaus < X nucleotides in length |
200 |
rje_samtools |
dirnlen=X |
Include directional read length data at X bp intervals (readlen=T; 0=OFF) |
500 |
rje_samtools |
fdrcut=X |
Additional FDR cutoff for enriched treatment SNPs |
1.0 |
rje_samtools |
fullcut=X |
Proportion of read to be mapped to count as full-length |
0.9 |
rje_samtools |
majcut=X |
Frequency cutoff for Major allele |
0.0 |
rje_samtools |
mincut=X |
Minimum read count for minor allele (proportion if <1) |
1 |
rje_samtools |
minqn=X |
Min. number of reads meeting qcut (QN) for output |
10 |
rje_samtools |
peaksmooth=X |
Smooth out Xcoverage peaks < X depth difference to flanks (<1 = %Median) |
0.05 |
rje_samtools |
qcut=X |
Min. quality score for a call to include |
30 |
rje_samtools |
sigcut=X |
Significance cutoff for enriched treatment SNPs |
0.05 |
rje_samtools_V0 |
minfreq=X |
Minor allele(s) frequency correction for zero counts (e.g. Sequencing error) |
0.001 |
rje_samtools_V0 |
qcut=X |
Min. quality score for a call to include |
40 |
rje_seq |
alnprog=X |
Choice of alignment program to use (clustalw/clustalo/muscle/mafft/fsa/pagan) |
clustalo |
rje_seq |
maxgap=X |
Maximum proportion of sequence that may be gaps (<=0 = No maximum) |
0 |
rje_seq |
maxglob=X |
Maximum proportion of sequence predicted to be ordered (<=0 = None; >=1 = Absolute) |
0 |
rje_seq |
maxlen=X |
Maximum length of sequences (<=0 = No maximum) |
0 |
rje_seq |
maxx=X |
Maximum proportion of sequence that may be Xs (<=0 = No maximum; >=1 = Absolute no.) |
0 |
rje_seq |
minlen=X |
Minimum length of sequences |
0 |
rje_seq |
minorf=X |
Minimum ORF length for a DNA/EST translation (reformatting only) |
0 |
rje_seq |
minpoly=X |
Minimum length of poly-A tail for 3rf / 6rf EST translation (reformatting only) |
20 |
rje_seq |
nrid=X |
%Identity cut-off for Non-Redundancy (GABLAMO) |
100.0 |
rje_seq |
nrsim=X |
%Similarity cut-off for Non-Redundancy (GABLAMO) |
None |
rje_seq |
ntrim=X |
Trims of regions >= X proportion N bases (X residues for protein) |
0.0 |
rje_seq |
query=X |
Selects query sequence by name |
None |
rje_seq |
relconwin=X |
Window size for relative conservation scoring |
30 |
rje_seq |
seqname=X |
Output sequence names for PNG files etc. (short/Name/Number/AccNum/ID) |
short |
rje_seq |
seqtype=X |
Force program to read as DNA, RNA, Protein or Mixed (case insensitive; read=Will work it out) |
None |
rje_seq |
trunc=X |
Truncates each sequence to the first X aa. (Last X aa if -ve) (Useful for webservers like SingalP.) |
0 |
rje_seqgen |
idmax=X |
Max number for randseq ID. If < seqnum, will use seqnum. If <0, no zero-prefixing of IDs. |
0 |
rje_seqgen |
idmin=X |
Starting numerical ID for randseq (allows appending) |
1 |
rje_seqgen |
markovx=X |
Order of markov chain to use for sequence construction |
1 |
rje_seqgen |
maxhyd=X |
Maximum mean hydrophobicity score |
10 |
rje_seqgen |
poolcyc=X |
Number of times to retry making sequences if rules are broken |
1 |
rje_seqgen |
randname=X |
Name 'leader' for output fasta file |
randseq |
rje_seqgen |
scramblecyc=X |
Number of attempts to try each scramble before giving up |
10000 |
rje_seqgen |
screenx=X |
Reject generated sequences containing screened Xmers >= X |
0 |
rje_seqgen |
seqnum=X |
Number of random sequences to generate |
24 |
rje_seqgen |
teiresias=X |
Length of patterns to be screened by additional TEIRESIAS search on scrambled vs original |
0 |
rje_seqlist |
maxlen=X |
Maximum length of sequences (<=0 = No maximum) |
0 |
rje_seqlist |
minlen=X |
Minimum sequence length |
0 |
rje_seqlist |
minorf=X |
Min. ORF length for translated sequences output. -1 for single translation inc stop codons |
-1 |
rje_seqlist |
newacc=X |
New base for sequence accession numbers - will rename sequences |
None |
rje_seqlist |
newgene=X |
New gene for renamed sequences (if blank will use newacc or 'seq' if none read) |
None |
rje_seqlist |
reformat=X |
Output format for sequence files (fasta/short/acc/acclist/speclist/index/dna2prot/peptides/(q)region/revcomp) |
fasta |
rje_seqlist |
rftran=X |
No. reading frames (RF) into which to translate (1,3,6) |
1 |
rje_seqlist |
sampler=N(,X) |
Generate (X) file(s) sampling a random N sequences from input into seqout.N.X.fas |
0 |
rje_seqlist |
seqformat=X |
Expected format of sequence file |
None |
rje_seqlist |
seqmode=X |
Sequence mode, determining method of sequence storage (full/list/file/index/db/filedb). |
file |
rje_seqlist |
seqtype=X |
Sequence type (prot(ein)/dna/rna/mix(ed)) |
None |
rje_seqlist |
sortseq=X |
Whether to sort sequences prior to output (size/invsize/accnum/name/seq/species/desc) |
None |
rje_seqlist |
spcode=X |
Species code for non-gnspacc format sequences |
None |
rje_seqlist |
split=X |
String to be inserted between each concatenated sequence |
'' |
rje_seqlist |
splitseq=X |
Split output sequence file according to X (gene/species) |
None |
rje_seqlist |
terminorf=X |
Min. length for terminal ORFs, only if no minorf=X ORFs found (good for short sequences) |
-1 |
rje_seqplot |
outfile=X |
Leader for output files |
None |
rje_seqplot |
plotwin=X |
Window for stats plot +/- |
7 |
rje_sleeper |
sleep=X |
Seconds to sleep for between prints |
600 (10 mins) |
rje_sleeper |
wake=X |
Total seconds until finishing |
864,000 (10 days) |
rje_slim |
ambcut=X |
Cut-off for max number of choices in ambiguous position to be shown as variant (0=All) |
10 |
rje_slimcalc |
alnext=X |
File extension of alignment files, AccNum.X (checked before Gopher used) |
orthaln.fas |
rje_slimcalc |
conscore=X |
Type of conservation score used: |
rlc |
rje_slimcalc |
consweight=X |
Weight given to global percentage identity for conservation, given more weight to closer sequences |
0 |
rje_slimcalc |
iucut=X |
Cut-off for IUPred results (0.0 will report mean IUPred score) |
0.0 |
rje_slimcalc |
iumethod=X |
IUPred method to use (long/short) |
short |
rje_slimcalc |
minhom=X |
Minimum number of homologues for making conservation score |
1 |
rje_slimcalc |
percentile=X |
Percentile steps to return in addition to mean |
0 |
rje_slimcalc |
relconwin=X |
Window size for relative conservation scoring |
30 |
rje_slimcalc |
winsize=X |
Used to define flanking regions for calculations. If negative, will use flanks *only* |
0 |
rje_slimcore |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
rje_slimcore |
casemask=X |
Mask Upper or Lower case |
None |
rje_slimcore |
equivcut=X |
BLOSUM score cut-off for equivalence groups |
1 |
rje_slimcore |
homcut=X |
Max number of homologues to allow (to reduce large multi-domain families) |
0 |
rje_slimcore |
masktext=X |
Text ID to over-ride automated masking text and identify specific masking settings |
None |
rje_slimcore |
maxseq=X |
Maximum number of sequences to process |
0 |
rje_slimcore |
maxupc=X |
Maximum UPC size of dataset to process |
0 |
rje_slimcore |
megaslimdp=X |
Accuracy (d.p.) for MegaSLiM masking tool raw scores |
4 |
rje_slimcore |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
rje_slimcore |
randbase=X |
Base for random dataset name |
rand |
rje_slimcore |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
rje_slimcore |
sizesort=X |
Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) |
0 |
rje_slimcore |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
rje_slimfungo |
minocc=X |
Min occurrences for a motif in a GO category |
6 |
rje_slimhtml |
border=X |
Border setting for tables |
0 |
rje_slimhtml |
xgcut=X |
Significance cut-off for XGMML |
0.01 |
rje_slimlist |
alnext=X |
File extension of alignment files, accnum.X |
aln.fas |
rje_slimlist |
ambcut=X |
Cut-off for max number of choices in ambiguous position to be shown as variant |
10 |
rje_slimlist |
flanksize=X |
Size of sequence flanks for motifs |
30 |
rje_slimlist |
iucut=X |
Cut-off for IUPred results (0.0 will report mean IUPred score) |
0.0 |
rje_slimlist |
iumethod=X |
IUPred method to use (long/short) |
short |
rje_slimlist |
minfix=X |
Min number of fixed positions for a motif to contain |
0 |
rje_slimlist |
minic=X |
Min information content for a motif (1 fixed position = 1.0) |
0.0 |
rje_slimlist |
minpos=X |
Min number of defined positions |
0 |
rje_slimlist |
percentile=X |
Percentile steps to return in addition to mean |
0 |
rje_slimlist |
winsize=X |
Used to define flanking regions for stats. If negative, will use flanks *only* |
0 |
rje_slimlist |
xdivide=X |
Size of dividing Xs between motifs |
10 |
rje_ssds |
strand=X |
Strand for RACE primers -1 (3'), 1 (5') or 0 (both) |
0 |
rje_synteny |
tophitbuffer=X |
Percentage identity difference to keep best hits for reference genes/proteins. |
1.0 |
rje_taxamap |
basefile=X |
Base for output files. Will reuse unless force=T |
'taxmap' |
rje_taxamap |
bootfilter=X |
Filter bootstrap support < X to "Uncertain" |
0.0 |
rje_taxamap |
minboot=X |
Minimum bootstrap value for an "in-clade" with query protein |
0.5 |
rje_taxamap |
minclass=X |
Convert taxa with score < minclass to "Other" for *.CLASS.tdt output |
1.0 |
rje_taxamap |
minscore=X |
Filter out species codes with score < minscore |
1.0 |
rje_taxamap |
minsum=X |
Convert taxa with score < minsum to "Other" for *.taxsum.tdt output |
10.0 |
rje_taxamap |
noneboot=X |
Bootstrap support to give "None" ratings |
1.0 |
rje_taxamap |
taxbase=X |
Base of previous run to load results from, if not basefile |
|
rje_taxonomy |
basefile=X |
Results file prefix. Will use first taxin=LIST term if missing |
None |
rje_tm |
source=X |
Source text for mySQL file |
'tmhmm' |
rje_tree |
bootstraps=X |
Number of bootstraps |
0 |
rje_tree |
deflen=X |
Default branch length (when none given, also for tree scaling) |
0.1 |
rje_tree |
fam=X |
minimum number of families (If 0, no subfam grouping) |
0 |
rje_tree |
groupspec=X |
Species for duplication grouping |
None |
rje_tree |
maketree=X |
Program for making tree |
None |
rje_tree |
mfs=X |
minimum family size |
3 |
rje_tree |
outnames=X |
'short'/'long' names in output file |
short |
rje_tree |
rootbuffer=X |
Min. distance from node for root placement (percentage of branch length) |
0.1 |
rje_tree |
savetype=X |
Format for generated tree file (nsf/nwk/text/r/png/bud/qspec/cairo/te/svg/html) |
nwk |
rje_tree |
specdup=X |
Minimum number of different species in clade to be identified as a duplication |
1 |
rje_tree |
textscale=X |
Default scale for text trees (no. of characters per deflen distance) |
4 |
rje_tree |
truncnames=X |
Truncate names to X characters (0 for no truncation) |
123 |
rje_uniprot |
accfield=X |
Accession number field for acctable=FILE extraction |
UniProt |
rje_uniprot |
basefile=X |
If set, can use "T" or "True" for other `*out` options. (Will default to `datout` if given) |
None |
rje_uniprot |
lcft=X |
Feature to add for LowerCase portions of sequence |
|
rje_uniprot |
specsleep=X |
Sleep for X seconds between species downloads |
60 |
rje_uniprot |
ucft=X |
Feature to add for UpperCase portions of sequence |
|
rje_uniprot |
uniformat=X |
Desired UniProt format for URL download (over-rules normal processing). Append gz to compress. |
txt |
rje_xref |
basefile=X |
Basefile for output files |
Default: filexref or first xrefdata input file w/o path |
rje_xref |
keyid=X |
Key field header to be used in main Data dictionary - aliases map to this |
'Gene' |
rje_xref |
mapfields=X |
Fields to be used for Alias mapping plus KeyID. (Must be in XRef). |
|
rje_xref |
splitchar=X |
Character on which to split fields for multiple alias processing |
'|' |
rje_zen |
wisdoms=X |
Number of Zen Wisdoms to return |
10 |
rje_zen |
zensleep=X |
Time in seconds to sleep between wisdoms |
0 |
samphaser |
absmincut=X |
Absolute minimum read count for minor allele (used if mincut<1) |
2 |
samphaser |
absphasecut=X |
Absolute minimum read count for phasecut (used if phasecut<1) |
5 |
samphaser |
absunzipcut=X |
Absolute minimum read count for unzipcut (used if unzipcut<1) |
3 |
samphaser |
endmargin=X |
Extend block ends within X nucleotides of sequence ends |
10 |
samphaser |
mincut=X |
Minimum read count for minor allele (proportion of QN if <1) for pileup parsing |
0.1 |
samphaser |
minhapx=X |
Minimum mean coverage for haplotig |
5 |
samphaser |
minsnp=X |
Min number of SNPs per phased haplotype block |
5 |
samphaser |
phasecut=X |
Minimum read count for minor allele for phasing (proportion of QN if <1) |
0.25 |
samphaser |
snpcalc=X |
Max number of SNPs to use for read probability calculations (fewer = quicker) |
10 |
samphaser |
snperr=X |
Probability of an incorrect (biallelic) SNP call for individual read nucleotides |
0.05 |
samphaser |
splitzero=X |
Whether to split haplotigs at zero-coverage regions of X+ bp (-1 = no split) |
100 |
samphaser |
trackprob=X |
Min probability for assigning a read/SNP to Track A/B |
0.95 |
samphaser |
unzipcut=X |
Minimum read count for allele for unzipping haplotigs (proportion of QN if <1) |
0.1 |
seqforker |
forks=X |
Number of parallel sequences to process at once |
0 |
seqforker |
i=X |
Sets interactivity (-1 for full auto) |
0 |
seqforker |
killforks=X |
Number of seconds of no activity before killing all remaining forks. |
3600 |
seqforker |
outcmd=X |
Command line option for giving output file name. Will be altered to match forked splits (*.*) |
None |
seqforker |
seqincmd=X |
Command given to program for input file name |
seqin= |
seqforker |
split=X |
Number of sequences per split file |
0 |
seqforker |
startfrom=X |
Will pick up program at this sequence, where X is the name or accession number |
None |
seqforker |
v=X |
Sets verbosity (-1 for silent) |
0 |
seqmapper |
automap=X |
Minimum value of mapstat for automatic mapping to occur (if i<1) |
99.5 |
seqmapper |
blaste=X |
E-Value cut-off for BLAST searches (BLAST -e X) |
1e-4 |
seqmapper |
blastv=X |
Number of BLAST hits to return per query (BLAST -v X) |
20 |
seqmapper |
delimit=X |
Delimiter for *.mapping.* file (will set extension) |
tab |
seqmapper |
i=X |
Set interactivity. i=-1 full auto. i=0 no menu. i=1 interactive menu. |
1 |
seqmapper |
mapfocus=X |
Focus for mapping statistic, i.e. which sequence must meet requirements |
query |
seqmapper |
mapspec=X |
Maps sequences onto given species code. "Self" = same species as query. "None" = any. |
None |
seqmapper |
mapstat=X |
GABLAM Stat to use for mapping assessment (if GABLAM in mapping list) (ID/Sim/Len) |
ID |
seqmapper |
minmap=X |
Minimum value of mapstat for any mapping to occur |
90.0 |
seqmapper |
startfrom=X |
Shortname or AccNum of seqin file to startfrom (will append results) (memsaver=T only) |
None |
seqsuite |
batcharg=X |
Commandline argument to use for batchrun files |
'seqin' |
seqsuite |
batchlog=X |
Generate separate basefile.X log files for each batch run file (None for single log) |
log |
seqsuite |
prog=X |
Identifies the tool to be used. Will load defaults from X.ini (before seqsuite.ini) |
seqlist |
slim_pickings |
advmax=X |
Max number of sequences to use computationally intensive advanced probability |
35 |
slim_pickings |
alnext=X |
File extension of alignment files, accnum.X |
orthaln.fas |
slim_pickings |
delimit=X |
Change delmiter to X |
, |
slim_pickings |
flanksize=X |
Size of sequence flanks for motifs |
30 |
slim_pickings |
iucut=X |
Cut-off for IUPred results |
0.2 |
slim_pickings |
iumethod=X |
IUPred method to use (long/short) |
short |
slim_pickings |
percentile=X |
Percentile steps to return in addition to mean |
0 |
slim_pickings |
picksid=X |
Outputs an extra 'PicksID' column containg the identifier X |
|
slim_pickings |
rankstat=X |
Stat to use to re-rank data |
RScore |
slim_pickings |
rerank=X |
Re-ranks according to RScore (if expect=T) and only outputs top X new ranks (if > 0) |
5000 |
slim_pickings |
slimranks=X |
Maximum number of SlimDisc ranks to exract from any given dataset |
5000 |
slim_pickings |
slimversion=X |
SLiMDisc results version for compiled output |
1.4 |
slim_pickings |
windis=X |
Number of aa to extend disorder prediction each side of occurrence |
0 |
slim_pickings |
winhyd=X |
Number of aa to extend Eisenberg Hydrophobicity calculation either side of motif |
0 |
slim_pickings |
winsa=X |
Number of aa to extend Surface Accessibility calculation either side of motif |
0 |
slim_pickings |
xdivide=X |
Size of dividing Xs between motifs |
10 |
slimbench |
benchbase=X |
Basefile for SLiMBench benchmarking output |
slimbench |
slimbench |
bycloud=X |
Whether to compress results into clouds prior to assessment (True/False/Both) |
Both |
slimbench |
datatype=X |
Type of data to be generated and/or benchmarked (occ/elm/ppi/dom/sim/simonly) |
elm |
slimbench |
filterdir=X |
Directory suffix for filtered benchmarking datasets |
_Filtered/ |
slimbench |
itype=X |
Interaction identifer for PPI datasets |
first element of ppisource |
slimbench |
maxseq=X |
Maximum number of randsource sequences for SLiM to hit (also maxaa and maxupc limits) |
1000 |
slimbench |
minic=X |
Min information content for a motif (1 fixed position = 1.0) |
2.0; 1.1 for OccBench |
slimbench |
minupc=X |
Minimum number of UPC for benchmark dataset |
3 |
slimbench |
ppid=X |
PPI source protein identifier type (gene/uni/none; will work out from headers if None) |
None |
slimbench |
ppisource=X |
Source of PPI data. (See documentation for details.) (HINT/FILE) |
'HINT' |
slimbench |
randbase=X |
Base for random dataset name if simbench=F |
ran |
slimbench |
randreps=X |
Number of replicates for each random (or simulated) datasets |
8 |
slimbench_V1 |
benchbase=X |
Basefile for SLiMBench benchmarking output |
slimbench |
slimbench_V1 |
bycloud=X |
Whether to compress results into clouds prior to assessment (True/False/Both) |
Both |
slimbench_V1 |
datatype=X |
Type of data to be generated and/or benchmarked (elm/sim/simonly) |
elm |
slimbench_V1 |
minic=X |
Min information content for a motif (1 fixed position = 1.0) |
2.0 |
slimbench_V1 |
minupc=X |
Minimum number of UPC for ELM dataset |
True |
slimbench_V1 |
randbase=X |
Base for random dataset name if simulate=F |
ran |
slimbench_V1 |
randreps=X |
Number of replicates for each random (or simulated) datasets |
10 |
slimdip |
dipmode=X |
Run mode for SLiMDip (slimdip/mimicry/enrichment/legacy) |
slimdip |
slimdip |
edgeswap=X |
Number of times to swap edges (x edge number) for edge swap method |
10 |
slimdip |
randbase=X |
This is the base of the randbase.X.tdt shuffled PPI files |
BASEFILE.rand |
slimdip |
randmethod=X |
Method for randomisation (shuffle/edgeswap) |
shuffle |
slimdip |
randppi=X |
Number of random PPI datasets to generate for enrichment analysis |
1000 |
slimdip |
runid=X |
RunID for SLiMProb run. (Can also extract from SLiMProb occ.csv file |
SLiMDIP |
slimfarmer |
basefile=X |
Set the log, RunID, ResFile, ResDir and Job to X |
None |
slimfarmer |
dependhpc=X |
Name of HPC system for depend |
'blue30.iridis.soton.ac.uk' |
slimfarmer |
email=X |
Email address to email job stats to at end |
'' |
slimfarmer |
farm=X |
Execute a special SLiMFarm analysis on HPC |
batch |
slimfarmer |
forks=X |
Number of forks to be used when hpcmode=fork and qsub=F. |
1 |
slimfarmer |
hpc=X |
Name of HPC system |
'katana' |
slimfarmer |
hpcmode=X |
Mode to be used for farming jobs between nodes (rsh/fork) |
fork |
slimfarmer |
iolimit=X |
Limit of number of IOErrors before termination |
50 |
slimfarmer |
job=X |
Name of job file (.job added) |
slimfarmer |
slimfarmer |
keepfree=X |
Number of processors to keep free on head node |
1 |
slimfarmer |
memfree=X |
Min. proportion of node memory to be free before spawning job |
0.1 |
slimfarmer |
nodes=X |
Number of nodes to run on |
1 |
slimfarmer |
pause=X |
Wait X seconds before attempting showstart |
5 |
slimfarmer |
pickhead=X |
Header to extract from OutList file and used to populate AccNum to skip |
|
slimfarmer |
ppn=X |
Processors per node |
16 |
slimfarmer |
runid=X |
Text identifier for SLiMSuite job farming |
`job` |
slimfarmer |
subsleep=X |
Sleep time (seconds) between cycles of subbing out jobs to hosts |
1 |
slimfarmer |
vmem=X |
Virtual Memory limit for run (GB) |
126 |
slimfarmer |
walltime=X |
Walltime for qsub job (hours) |
12 |
slimfinder |
absmin=X |
Used if minocc<1 to define absolute min. UP occ |
3 |
slimfinder |
absminamb=X |
Used if ambocc<1 to define absolute min. UP occ |
2 |
slimfinder |
ambocc=X |
Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) |
0.05 |
slimfinder |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
slimfinder |
casemask=X |
Mask Upper or Lower case |
None |
slimfinder |
clouds=X |
Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) |
2 |
slimfinder |
extras=X |
Whether to generate additional output files (alignments etc.) |
1 |
slimfinder |
focusocc=X |
Motif must appear in X+ focus groups (0 = all) |
0 |
slimfinder |
homcut=X |
Max number of homologues to allow (to reduce large multi-domain families) |
0 |
slimfinder |
maxseq=X |
Maximum number of sequences to process |
500 |
slimfinder |
maxupc=X |
Maximum UPC size of dataset to process |
0 |
slimfinder |
maxwild=X |
Maximum number of consecutive wildcard positions to allow |
2 |
slimfinder |
minic=X |
Minimum information content for returned motifs |
2.1 |
slimfinder |
minocc=X |
Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) |
0.05 |
slimfinder |
minwild=X |
Minimum number of consecutive wildcard positions to allow |
0 |
slimfinder |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
slimfinder |
probcut=X |
Probability cut-off for returned motifs (sigcut=X also recognised) |
0.1 |
slimfinder |
probscore=X |
Score to be used for probability cut-off and ranking (Prob/Sig/S/R) |
Sig |
slimfinder |
randbase=X |
Base for random dataset name |
rand |
slimfinder |
runid=X |
Run ID for resfile (allows multiple runs on same data) |
DATE |
slimfinder |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
slimfinder |
sizesort=X |
Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) |
0 |
slimfinder |
slimlen=X |
Maximum length of SLiMs to return (no. non-wildcard positions) |
5 |
slimfinder |
topranks=X |
Will only output top X motifs meeting probcut |
1000 |
slimfinder |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
slimfinder_V4.9 |
absmin=X |
Used if minocc<1 to define absolute min. UP occ |
3 |
slimfinder_V4.9 |
absminamb=X |
Used if ambocc<1 to define absolute min. UP occ |
2 |
slimfinder_V4.9 |
ambocc=X |
Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) |
0.05 |
slimfinder_V4.9 |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
slimfinder_V4.9 |
casemask=X |
Mask Upper or Lower case |
None |
slimfinder_V4.9 |
clouds=X |
Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) |
2 |
slimfinder_V4.9 |
extras=X |
Whether to generate additional output files (alignments etc.) |
1 |
slimfinder_V4.9 |
focusocc=X |
Motif must appear in X+ focus groups (0 = all) |
0 |
slimfinder_V4.9 |
homcut=X |
Max number of homologues to allow (to reduce large multi-domain families) |
0 |
slimfinder_V4.9 |
maxseq=X |
Maximum number of sequences to process |
500 |
slimfinder_V4.9 |
maxupc=X |
Maximum UPC size of dataset to process |
0 |
slimfinder_V4.9 |
maxwild=X |
Maximum number of consecutive wildcard positions to allow |
2 |
slimfinder_V4.9 |
minic=X |
Minimum information content for returned motifs |
2.1 |
slimfinder_V4.9 |
minocc=X |
Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) |
0.05 |
slimfinder_V4.9 |
minwild=X |
Minimum number of consecutive wildcard positions to allow |
0 |
slimfinder_V4.9 |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
slimfinder_V4.9 |
probcut=X |
Probability cut-off for returned motifs (sigcut=X also recognised) |
0.1 |
slimfinder_V4.9 |
probscore=X |
Score to be used for probability cut-off and ranking (Prob/Sig/S/R) |
Sig |
slimfinder_V4.9 |
randbase=X |
Base for random dataset name |
rand |
slimfinder_V4.9 |
runid=X |
Run ID for resfile (allows multiple runs on same data) |
DATE |
slimfinder_V4.9 |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
slimfinder_V4.9 |
sizesort=X |
Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) |
0 |
slimfinder_V4.9 |
slimlen=X |
Maximum length of SLiMs to return (no. non-wildcard positions) |
5 |
slimfinder_V4.9 |
topranks=X |
Will only output top X motifs meeting probcut |
1000 |
slimfinder_V4.9 |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
slimfrap |
fdranncut=X |
FDR cut-off for manual annotation |
0.05 |
slimgoer |
maxgenes=X |
Maximum number of genes for a GO term to apply to |
2000 |
slimgoer |
minhom=X |
Minimum number of homologues for each protein |
3 |
slimgoer |
minocc=X |
Minimum number of occurrences for a given Motif/GO combo |
5 |
slimjim |
htmlpng=X |
Graphic for corner of header frames - links back to Home |
'SBS_100.png' |
slimjim |
name=X |
Name of analysis |
'SLiMFinder Human PPI Analysis' |
slimjim |
suffix=X |
Suffix added to gene symbols for dataset name |
.ppi |
slimmaker |
ignore=X |
Amino acid(s) to ignore. (If nucleotide, would be N-) |
'X-' |
slimmaker |
maxaa=X |
Max. no. different amino acids for one position |
5 |
slimmaker |
minfreq=X |
Min. combined freq of accepted aa to avoid wildcard |
0.75 |
slimmaker |
minseq=X |
Min. no. of sequences for an aa to be in |
3 |
slimmaker |
peptalign=T/F/X |
Align peptides. Will use as guide regular expression, else T/True for regex-free alignment. |
True |
slimmutant |
maxmutant=X |
Maximum number of mutants for output |
100000 |
slimmutant |
minmutant=X |
Minimum number of mutants for output |
100 |
slimmutant |
mutfield=X |
Field in mutfile corresponding to AA subsitution data |
'AAChange' |
slimmutant |
mutflanks=X |
Generate for casemask=Upper of X aa flanking mutation (None if < 1) |
0 |
slimmutant |
ppisource=X |
Source of PPI data. (HINT/FILE) FILE needs 'Hub' and 'SpokeUni' fields. |
'HINT' |
slimmutant |
protfield=X |
Field in mutfile corresponding to protein accession number |
'Uniprot' |
slimmutant |
runid=X |
Limit analysis to SLiMProb RunID (blank = analyse all) |
|
slimmutant |
splitfield=X |
Field in mutfile to split data on (saved as basefile.X.tdt) |
|
slimparser |
maxrefresh=X |
Maximum number of seconds for incrementing check refresh |
600 |
slimparser |
password=X |
Optional password for REST jobid retrieval |
None |
slimparser |
refresh=X |
Initial number of seconds for between checks for job status (will double) |
5 |
slimparser |
rest=X |
Return text for just the REST output element X |
|
slimparser |
restbase=X |
Basefile for parsed REST output that lacks defined filename |
jobid |
slimparser |
resturl=X |
URL of rest server |
'http://rest.slimsuite.unsw.edu.au/' |
slimprob |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
slimprob |
casemask=X |
Mask Upper or Lower case |
None |
slimprob |
extras=X |
Whether to generate additional output files (alignments etc.) |
2 |
slimprob |
maxocc=X |
Filter out Motifs with more than maximum number of occurrences |
0 |
slimprob |
maxseq=X |
Maximum number of sequences to process |
0 |
slimprob |
maxsize=X |
Maximum dataset size to process in AA (or NT) |
100,000 |
slimprob |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
slimprob |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
slimprob |
seqocc=X |
Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) |
1 |
slimprob |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
slimprob_V1.4 |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
slimprob_V1.4 |
casemask=X |
Mask Upper or Lower case |
None |
slimprob_V1.4 |
extras=X |
Whether to generate additional output files (alignments etc.) |
2 |
slimprob_V1.4 |
maxocc=X |
Filter out Motifs with more than maximum number of occurrences |
0 |
slimprob_V1.4 |
maxseq=X |
Maximum number of sequences to process |
0 |
slimprob_V1.4 |
maxsize=X |
Maximum dataset size to process in AA (or NT) |
100,000 |
slimprob_V1.4 |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
slimprob_V1.4 |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
slimprob_V1.4 |
seqocc=X |
Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) |
1 |
slimprob_V1.4 |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
slimsearch |
blaste=X |
BLAST e-value threshold for determining relationships |
1e=4 |
slimsearch |
casemask=X |
Mask Upper or Lower case |
None |
slimsearch |
extras=X |
Whether to generate additional output files (alignments etc.) |
1 |
slimsearch |
maxocc=X |
Filter out Motifs with more than maximum number of occurrences |
0 |
slimsearch |
maxseq=X |
Maximum number of sequences to process |
0 |
slimsearch |
maxsize=X |
Maximum dataset size to process in AA (or NT) |
100,000 |
slimsearch |
motifmask=X |
List (or file) of motifs to mask from input sequences |
|
slimsearch |
savespace=0 |
Delete "unneccessary" files following run (best used with targz): |
0 |
slimsearch |
seqocc=X |
Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) |
1 |
slimsearch |
walltime=X |
Time in hours before program will abort search and exit |
1.0 |
slimsuite |
prog=X |
Identifies the tool to be used. Will load defaults from X.ini (before slimsuite.ini) |
help |
smrtscape |
avread=X |
Average read length (bp) |
20000 |
smrtscape |
errperbase=X |
Error-rate per base |
0.14 |
smrtscape |
lenfilter=X |
Min read length for filtered subreads |
5000 |
smrtscape |
mapefficiency=X |
Efficiency of mapping anchor subreads onto seed reads for correction |
0.8 |
smrtscape |
maxcov=X |
Maximum X coverage to calculate for coverage=T analysis |
100 |
smrtscape |
minanchorx=X |
Minimum X coverage for anchor (preassembly error-correcting) subreads |
6 |
smrtscape |
minreadlen=X |
Absolute minimum read length for calculations (use minlen=X to affect summary also) |
500 |
smrtscape |
rqfilter=X |
Min read quality for filtered subreads |
0.85 |
smrtscape |
rqstep=X |
Size of RQ jumps for calculation (min 0.001) |
0.01 |
smrtscape |
smrtreads=X |
Average assemble output of a SMRT cell |
50000 |
smrtscape |
smrtunits=X |
Units for smrtreads=X (reads/Gb/Mb) |
reads |
smrtscape |
targetxcov=X |
Target 100% X Coverage for pre-assembly (e.g. error-corrected seed reads) |
3 |
smrtscape |
xmargin=X |
"Safety margin" inflation of desired minimum X coverage |
1 |
smrtscape |
xsteplen=X |
[Adv.] Size (bp) of increasing coverage steps for calculating required depths of coverage |
1e5 |
smrtscape_V1 |
avread=X |
Average read length (bp) |
20000 |
smrtscape_V1 |
errperbase=X |
Error-rate per base |
0.14 |
smrtscape_V1 |
genomesize=X |
Genome size (bp) |
0 |
smrtscape_V1 |
mapefficiency=X |
[Adv.] Efficiency of mapping anchor subreads onto seed reads for correction |
1.0 |
smrtscape_V1 |
maxcov=X |
Maximum X coverage to calculate |
100 |
smrtscape_V1 |
minanchorx=X |
Minimum X coverage for anchor subreads |
6 |
smrtscape_V1 |
minreadlen=X |
Absolute minimum read length for calculations (use minlen=X to affect summary also) |
500 |
smrtscape_V1 |
rqstep=X |
Size of RQ jumps for calculation (min 0.001) |
0.01 |
smrtscape_V1 |
smrtreads=X |
Average assemble output of a SMRT cell |
50000 |
smrtscape_V1 |
smrtunits=X |
Units for smrtreads=X (reads/Gb/Mb) |
reads |
smrtscape_V1 |
targetcov=X |
Target percentage coverage for final genome |
99.999 |
smrtscape_V1 |
targeterr=X |
Target errors per base for preassembly |
1/genome size |
smrtscape_V1 |
targetxcov=X |
Target 100% X Coverage for pre-assembly |
3 |
smrtscape_V1 |
xmargin=X |
"Safety margin" inflation of X coverage |
1 |
smrtscape_V1 |
xsteplen=X |
[Adv.] Size (bp) of increasing coverage steps for calculating required depths of coverage |
1e5 |
snapper |
localmin=X |
Minimum length of local alignment to output to local stats table |
10 |
snapper |
localsort=X |
Local hit field used to sort local alignments for localunique reduction |
Identity |
snapper |
nocopylen=X |
Minimum length for CNV=0 fragments to be output |
100 |
snapper |
nocopymerge=X |
CNV=0 fragments within X nt of each other will be merged prior to output |
20 |
snapper |
spcode=X |
Overwrite species read from file (if any!) with X if generating sequence file from genbank |
None |
snp_mapper |
spcode=X |
Overwrite species read from file (if any!) with X if generating sequence file from genbank |
None |
spydarm |
backbase=X |
Prefix of backed up output files for previous release |
slimsuite.#DATE |
spydarm |
basefile=X |
Prefix for output files |
slimsuite |
spydarm |
prevbase=X |
Prefix of output files for previous release (to update) |
slimsuite |
trex |
endbuffer=X |
Max distance from end of sequence to flag repeat for trimming |
100 |
trex |
trimflank=X |
Additional flanking nucleotides to trim off the end of the sequence |
200 |
trex |
trmode=X |
How to handle terminal tandem repeats (keep/trim/iterate) |
keep |
unifake |
disdom=X |
Disorder threshold below which to annotate PFam domain as "DOMAIN" |
0.0 |
unifake |
spcode=X |
Species code to use if it cannot be established from sequence name |
None |