Hi So I've been using HOMER to perform motif enrichment analysis in a set of regions (BED file) and I'm getting nice enriched motifs. I think the output of findMotifsGenome.pl is fine, but I'm struggling to make a final analysis. I would like to know which motifs are present in which regions. I have seen in some papers where they report the different motif instances in the different regions. I'm sure it's easy enough to do that but I cannot find how to do it. How could one determine the instances of the motfis present at the regions, I guess coming from the output .motif files from findMotifsGenome.pl
Thank you four your help!
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written
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nanoide
2 answers
You can use programs that scans the genome for a given motif. For example, FIMO from MEME or matrix-scan from rsat or bioconductor packages like motiftatchr or TFBS Tools
motifmatchr is based on MOODS
Some answers I've written on searching promoters for TFBS using FIMO could apply here, where you replace promoters with peaks. These answers walk through use of FIMO step-by-step.
You could adjust this answer for your regions-of-interest, organism, assembly, and TF databases-of-interest.
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