Question: Getting motif instances corresponding to regions
0
gravatar for nanoide
12 months ago by
nanoide40
nanoide40 wrote:

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!

ADD COMMENTlink modified 12 months ago by Alex Reynolds29k • written 12 months ago by nanoide40
3
gravatar for geek_y
12 months ago by
geek_y10k
Barcelona
geek_y10k wrote:

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

ADD COMMENTlink modified 12 months ago • written 12 months ago by geek_y10k

Thanks for your response!

ADD REPLYlink written 12 months ago by nanoide40
2
gravatar for Alex Reynolds
12 months ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

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.

ADD COMMENTlink written 12 months ago by Alex Reynolds29k

Thanks, appreciate it!

ADD REPLYlink written 12 months ago by nanoide40
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