MEME tools for ATAC-seq peaks

[Teshome Mulugeta]

Hi,

I would like to search overrepresented motifs in over 120,000 peaks. Is there any tool in meme-suite that is suitable to this? Can meme-chip handle atac-seq peaks too?  Any further advice who has done similar task will be appreciated.

Best,
Teshome

[CharlesEGrant]

MEME-ChiIP is the appropriate tool. It was designed for the analysis of motifs in ChIP-Seq experiments. A protocol for using MEME-ChIP is here.