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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
| Module | Option | Description | Default |
|---|---|---|---|
| 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.