Getting motif instances corresponding to regions

Question

[nanoide]

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!

Answer 1

[GouthamAtla]

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

[nanoide]

Thanks for your response!

Answer 2

[Alex Reynolds]

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.

TFBS enrichiment analysis

https://bioinformatics.stackexchange.com/questions/2467/where-to-download-jaspar-tfbs-motif-bed-file/2491#2491

You could adjust this answer for your regions-of-interest, organism, assembly, and TF databases-of-interest.

[nanoide]

Thanks, appreciate it!