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SLiMSuite Documentation
Please note that command documentation sometimes lags behind the latest module versions. Click on module names to check current documentation.
cmd: seqin
Option Type: [?]{docs:?} FASFILE FILE SEQFILE
Modules: extatic orcfinder prothunter rje_mirna rje_pacbio rje_price rje_slimfungo samphaser scap slimdip trex rje_pattern_discovery rje_seqgen rje_seqplot rje_yeast seqforker sfmap2png gopher_V2 qslimfinder_V1.9 slimfinder_V4.9 slimprob_V1.4 rje_biogrid rje_genbank rje_hpc rje_iridis rje_markov rje_pam rje_samtools rje_seqlist rje_seq rje_slimcore rje_tm snp_mapper aphid budapest fiesta gablam gasp gfessa gopher haqesac multihaq picsi qslimfinder seqmapper slimfarmer slimfinder slimmutant slimprob slimsearch smrtscape_V1 smrtscape snapper unifake
| Module | Option | Description | Default |
|---|---|---|---|
| aphid | seqin=FILE |
Sequence file containing hits (if pepnorm != count) | None |
| budapest | seqin=FILE |
Name of EST fasta file used for search | None |
| extatic | seqin=FASFILE |
cDNA input seqence file (*.cdna.fas). See docs for naming advice. | ExTATIC.cdna.fas |
| fiesta | seqin=FILE |
EST file to be processed | None |
| gablam | seqin=FILE |
Query dataset file | infile.fas |
| gasp | seqin=FILE |
Fasta/ClustalW/Phylip Format sequence file | infile.fas |
| gfessa | seqin=FILE |
File containing EST/cDNA data to search for tags within | None |
| gopher | seqin=FILE |
Fasta file of 'query' sequences for orthology discovery (over-rides uniprotid=LIST) | |
| gopher_V2 | seqin=FILE |
Fasta file of 'query' sequences for orthology discovery | |
| haqesac | [seqin=?]{docs:?} |
? |
|
| multihaq | seqin=FILE |
Input query sequences | None |
| orcfinder | seqin=FILE |
Sequence file to search | None |
| picsi | seqin=FILE |
File containing sequences hit during searches | None |
| prothunter | [seqin=?]{docs:?} |
? |
|
| qslimfinder | seqin=FILE |
Sequence file to search | None |
| qslimfinder_V1.9 | seqin=FILE |
Sequence file to search | None |
| rje_biogrid | seqin=FILE |
Sequence file containing protein sequences with appropriate Accession Numbers/IDs | None |
| rje_genbank | seqin=FILE |
Input Genbank file | |
| rje_hpc | seqin=FILE |
Input sequence file to farm out | None |
| rje_iridis | seqin=FILE |
Input sequence file to farm out | None |
| rje_markov | seqin=FILE |
File with input sequences | None |
| rje_mirna | seqin=FILE |
Main file for analysis, containing UTRs | |
| rje_pacbio | seqin=FILE |
Subread sequence file for analysis | None |
| rje_pam | seqin=FILE |
Sequence file from which to calculate AA freq for scaling | None |
| rje_pattern_discovery | seqin=FILE |
Sequence File to search | None |
| rje_price | seqin=FILE |
Input sequence alignment in fasta format (over-rides batch=LIST) | None |
| rje_samtools | seqin=FASFILE |
Sequence file for loci in MPileup/SAM files (e.g. matching all relevant RID files) | None |
| rje_seq | seqin=FILE |
Loads sequences from FILE (fasta,phylip,aln,uniprot or fastacmd names from fasdb) | None |
| rje_seqgen | seqin=FILE |
Input sequence file to randomise | None |
| rje_seqlist | seqin=FILE |
Sequence input file name. | None |
| rje_seqplot | seqin=FILE |
File containing input sequences | None |
| rje_slimcore | seqin=FILE |
Sequence file to search. Over-rules batch mode (and uniprotid=LIST). | None |
| rje_slimfungo | seqin=FILE |
File of input sequences | None |
| rje_tm | seqin=FILE |
Sequence file for which predictions have been made | None |
| rje_yeast | seqin=FILE |
Input sequence file containing yeast sequences | Proteins.fas |
| samphaser | seqin=FASFILE |
Input genome to phase variants in | |
| scap | seqin=FILE |
File with input sequences for testing | None |
| seqforker | seqin=FILE |
Input sequence file | None |
| seqmapper | seqin=FILE |
File of sequences to be mapped | None |
| sfmap2png | seqin=FILE |
*.mapping.fas file to use as input data | |
| slimdip | seqin=FASFILE |
File containing spoke protein sequences. If not found, will generate from SpokeUni field | None |
| slimfarmer | seqin=FILE |
Input sequence file to farm out | None |
| slimfinder | seqin=SEQFILE |
Sequence file to search. Over-rules batch=FILE and uniprotid=LIST | None |
| slimfinder_V4.9 | seqin=FILE |
Sequence file to search | None |
| slimmutant | seqin=FILE |
Input file with protein sequences | |
| slimprob | seqin=SEQFILE |
Sequence file to search. Over-rules batch=FILE and uniprotid=LIST | None |
| slimprob_V1.4 | seqin=FILE |
Sequence file to search | None |
| slimsearch | seqin=FILE |
Sequence file to search | None |
| smrtscape | seqin=FILE |
Subread sequence file for analysis (over-rides batch command) | None |
| smrtscape_V1 | seqin=FILE |
Subread sequence file for analysis | None |
| snapper | seqin=FASFILE |
Input genome to identify variants in | |
| snp_mapper | seqin=FILE |
Sequence input file with accession numbers matching Locus IDs, or Genbank file. | |
| trex | seqin=FASFILE |
Fasta file of representative repeat sequences for removal | |
| unifake | seqin=FILE |
Input sequence file. See rje_seq documentation for filtering options. | None |
© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.