how do I use Homer with custom regions?

0

Entering edit mode

6.5 years ago

lavanya.kannan ▴ 20

Hi,

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.

Thanks

Homer • 1.9k views

ADD COMMENT • link 6.5 years ago by lavanya.kannan ▴ 20

0

Entering edit mode

Yes, are you sure that the findmotifs.pl command is even outputting the regions that you want to want to annotate? By default, annotatePeaks.pl should annotate 5' and 3' UTRs (if they exist in your input file).

ADD REPLY • link 6.5 years ago by Kevin Blighe 87k

Login before adding your answer.