MEME-CHIP Compare common MOTIFs across several samples

[Nachiket Shankar]

Hi All,

I'm doing a meta-analysis where I'm taking ChIP data from several datasets calling peaks, and then doing a denovo motif search of every sample. 

Ex: Input

Sample1, Sample2, Sample3 ..... Sample n

Output

Sample1.meme , Sample2.meme, Sample3.meme ... SampleN.meme

How do I compare across all these samples both reverse complement and regular to look for common motifs across several samples? 

[cegrant]

Tomtom is the MEME Suite tool for comparing motifs. You can combine the individual MEME files into a single file using the meme2meme script, which is included as part of the MEME Suite source. If you don't want to download and build MEME Suite you could also merge the files manually using any plain text editor (not a word processor like Microsoft Word). The required format is described here. 

Once you've merged the motifs into a single file you can submit it to Tomtom by using it for both the target and query motifs. Tomtom will evaluate the similarity of each possible pair of motifs. If you want to compare your de novo motifs to a collection of known motifs use your merged file as the query motif and the collection of known motifs as the target. You can upload your own collection of known motifs or use one of the collections we provide online for Tomtom.