Looking For Motif Finding Tools That Work On Broad Peaks

Question

[dfernan]

Hi,

I am profiling a chromatin regulator that covers relatively large areas of the genome, i.e., it's tracks do not look like sharp, narrow TFs, but more like the h3k27ac mark.

I am trying to find a suitable motif finder program for such type of marks. I'd like the input to the software to be a bed file (in my case ~ 20,000 relatively broad peaks) with the positions in the hg19 human genome.

Any advise is welcome, I'd love to try more than one program so I can compare the results.

Thanks!

Answer 1

[k.nirmalraman]

You can try the meme suite. But here you will need FASTA files as input, which is relatively easy to prepare from BED file as input when you have the genome.

Meme - ChiP or DREME can be used as per your needs. Detailed documentation is available here.

You may need a local installation of MEME Suite to run larger files.

Answer 2

[vj]

You can try HOMER software. It seems to work faster for larger genomic intervals as will be your case. You must use the -size option if you want to look for motifs for the whole interval.