search

jmschrei / tfmodisco-lite

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
MIT License
56 stars 16 forks source link

motifs.html report can be confusing #26

Open janewangsmile opened 1 year ago

janewangsmile commented 1 year ago

Hi,

When matching to tomtom, the motifs.html report can be very confusing for a few reasons:

  1. it also reports matches that are not significant, such as q-value =1
  2. when performing the match, it uses the ppm of the tfmodisco pattern to match known motifs in tomtom which also uses ppm, however, in the .html report, tfmodisco motif plot is based on attribution score. q-value are based on the ppm match. So, we can easily see cases that plots are not similar at all but q-values are very significant. plots and q-values are not consistently based on the same matrix.