Motif enrichment across super-enhancer regions

Question

[sk_24]

I have to find the motifs of specific transcription factors across the super-enhancer regions called using H3K27ac marks. I tried using HOMER findMotifsGenome.pl, but it is taking a lot of time. Since I have to find the motifs for only few transcription factors, what is an alternative way?

Answer 1

[rfran010]

I have found MEME-suite to be quick and easy to use: https://meme-suite.org/meme/index.html

To find motif occurrences, you can use FIMO.

To find motif enrichment you can use xstreme for de novo searches, or directly use SEA to check if known motifs are enriched.

You can use the database options for motifs, or only input motifs you care about in meme format.