I am interested in the common motifs in a set of genes that resulted from a DESeq2 analysis. I used the "findMotifs.pl" command of HOMER and got some motifs. Namely, I used findmotifs.pl genelist.txt mouse $outdir
Now, I am interested in annotating the motifs based on the location in which the motifs are located.
I ran the command annotatePeaks.pl tts mm10 -m $motif -list genelist.txt
The results of this is only motifs in the promoter region. How to I specify 3' or 5' in the above command. I am trying the -rna option instead of the tts option in the above command. This option did not give me any output. Should I try to change the -start and -end options in the findmotifs.pl command? If so, how far away either side of the tss should I go? The default options are -300 and 50 respectively.