Hi, I have two ChIP-seq bed files of same transcription factor. I want to compare one specific binding motif between these two ChIP-seq binding peaks, i.e. whether the motif is more enriched in the binding sites of one ChIP-seq vs. the other (under different culture condition)?

The plots I want to make is by X axis: "Distance from centre of ChIP region (bp)" and the Y axis: " No. motif / no. binding sites"

Thank you for your answers!

Xiaoyong
You can use MEME suite for enrichment of a specific motif over the given background (http://meme.nbcr.net/meme/tools/ame).. To plot the enrichment with distance, you will have to bin your input sequences into categories (1kb, 2kb, 3kb from TSS etc.), compute enrichment over control and then plot it in R with bins on X and enrichment score on Y axis..

Hope this helps.