neksa
commented
4 years ago I can see -t in advanced arguments (version 0.9.0):
--threshold THRESHOLD, -t THRESHOLD Significance threshold for qvalues, default value=0.05
TN is essentially two consecutive, independent tests: first T, then N. A means we consider all mutations in one test. I will simplify the help usage message. It's either T or N or A
Changed --save-motif-matches help
Currently thresholds "-t" are not included in "advanced arguments". We should also include thresholds on individual p-values.
I don’t think it is clear what “TN”, “NA”… mean; I would call these options “transcribed”,”non-transcribed”, “any” or “both” (“TN”?)
--save-motif-matches “save mutations in matching motifs to a BED file”