Open ThorbenMaa opened 11 months ago
@ivyraine would you mind taking a look when you have a chance?
I think here the for loop would need to be changed to also include negative patterns.
And within this for loop one could consider adding trimming of the motif :-). Because if you want to run fimo or tomtom with the untrimmed PWMs the results are very different (and strange) compared to the trimmed ones. And if I understand modisco correctly, when tomtom is used internally, modisco uses the trimmed motifs (probably for that reason).
I'll take a look soon, thanks for waiting
This worked for me to get all motifs out: