I also asked this question on SE bioinformatics, but since I didn't get any answers yet, I would like to ask it here as well. Hope you don't mind.
I have been using homer's
findMotifsGenome.pl, but with my new version (v4.9.1) of homer I don't get
.motif files in the knownResults folder. I do get them in the homerResults (de novo) folder, though. With my previous version of homer I did get them and used them to find which peaks are in which motif. Which is what I would like to do
Does anyone know why there are no
.motif files? I have only
.svg files. I have seen that for the homerResults the
.motif files are concatenated already into a file called
homerMotifs.all.motifs, but no such file for knownResults.
Does anyone know of this 'bug' in the new version of homer? Any solutions?
findMotifsGenome.pl All_peaks.txt Homo_sapiens.GRCh38.dna.primary_assembly.fa Peaks.All -p 20