Finding instances of motifs near peaks

Question

[Prakash]

Hi

I want to find instances of peaks near motif. I am using annotatePeaks.pl of HOMER. there is one option -m <motif file1> <motif file 2>.... Can anybody tell me what would be the format of this file.

Thanks in advance.

Answer 1

[Fidel]

I have not used annotatePeaks, but why don't you find the location of your motifs using FIMO from the MEME suite, and then use bedtools intersectBed to check which motif fall within the peak. I am assuming that you have a list of peaks as intervals (for example in bed format).

Answer 2

[Alex Reynolds]

Assuming inputs (peaks and motifs) are sorted BED files, you could use BEDOPS closest-features or bedmap to associate a motif with a nearest peak or set of nearby peaks, resp. You can use the same tools to do the inverse search: to associate a peak with its nearest TF binding site or set of overlapping sites.