SLiMSuite REST Server


Links
REST Home
EdwardsLab Homepage
EdwardsLab Blog
SLiMSuite Blog
SLiMSuite
Webservers
REST Pages
REST Status
REST Help
REST Tools
REST Alias Data
REST API
REST News
REST Sitemap

Option Type: minmax

Argument: compmask indexlen labels qregion region rq seqlen snptabmap xmers

Modules: rje_pacbio scap rje_mysql rje_seqgen qslimfinder_V1.9 slimfinder_V4.9 slimprob_V1.4 rje_markov rje_samtools rje_seqlist rje_slimcore haqesac qslimfinder slimfinder slimprob slimsearch smrtscape_V1 smrtscape

ModuleOptionDescriptionDefault
haqesac qregion=X,Y Concentrate on the region of the query from (and including) residue X to residue Y 0,-1
qslimfinder compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
qslimfinder qregion=X,Y Mask all but the region of the query from (and including) residue X to residue Y 0,-1
qslimfinder_V1.9 compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
qslimfinder_V1.9 qregion=X,Y Mask all but the region of the query from (and including) residue X to residue Y 0,-1
rje_markov [xmers=X[,Y]]{cmd:xmers} Deal with Xmers [upto Ymers] 1
rje_mysql indexlen=X,Y Will index all fields with non-numerics between X and Y letters by default 4,30
rje_pacbio rq=X,Y Minimum (X) and maximum (Y) values for read quality cutoffs 0.8,0.9
rje_samtools labels=X,Y Optional labels for Control and Treatment fields in output (other file basename used)
rje_samtools snptabmap=X,Y Optional SNPTable fields to replace for mapping onto FDR Locus,Pos fields (Locus,Pos)
rje_seqgen seqlen=X,Y Range of lengths for random sequences 10
rje_seqlist region=X,Y Alignment/Query region to use for reformat=peptides/(q)region reformatting of fasta alignment (1-L) 1,-1
rje_slimcore compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
rje_slimcore qregion=X,Y Mask all but the region of the query from (and including) residue X to residue Y 0,-1
scap [xmers=X[,Y]]{cmd:xmers} Deal with Xmers [upto Ymers] 1
slimfinder compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
slimfinder qregion=X,Y Mask all but the region of the query from (and including) residue X to residue Y 0,-1
slimfinder_V4.9 compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
slimfinder_V4.9 qregion=X,Y Mask all but the region of the query from (and including) residue X to residue Y 0,-1
slimprob compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) None
slimprob_V1.4 compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
slimsearch compmask=X,Y Mask low complexity regions (same AA in X+ of Y consecutive aas) 5,8
smrtscape rq=X,Y Minimum (X) and maximum (Y) values for read quality cutoffs 0.8,0.9
smrtscape_V1 rq=X,Y Minimum (X) and maximum (Y) values for read quality cutoffs 0.8,0.9

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.