Motif enrichment software?

[Cris Mar]

Hello,

What would be some good motif enrichment tools we can use/recommended?

I've tried MEME-ChIP and HOMER for RNA(i.e. iCLIP) but it seems I get very different results (despite paying attention to the strands).

Ideally I'd like to find motifs and then identify which crosslinks (i.e. gene) have the given motifs.

Thank you for any information. Hope everyone is staying safe!

Cris

[coy...@gmail.com]

I have just set up and run meme-chip to run locally for my eCLIP analysis.

I haven't tried HOMER.

I ran meme-chip vs. the human RBP motif dataset. You can get a gff file of the motifs and load that into IGV along with a bedgraph file of your peaks from CTK analysis.

You should further use bedtools intersect with that gff file and a genome features file to get genes containing motifs. I'll try this soon myself.

In my case, I was able to identify a motif that makes sense based on the biology of the protein and other research in the field, so I am somewhat confident in that motif.

Hope this is helpful, although it is not a direct answer.

Steve