common peaks and motifs between chip-seq replicates

[JenyaD]

Hi all!
I have 3 replicates of a chip-seq experiment, and after I used MACS for peak calling, I visualized the peaks on IGB. I see that there are common peaks between the replicates. Now, I would like to choose the common peaks of appropriate score between them and use a tool to look for possible enriched motifs. Could someone help in finding a good tool to do so?
Thanks!!!!

[SylvainL]

Hi,
with replicates for ChIPseq, the best would be to go with the ENCODE protocol (you can easily find with ENCODE ChIPseq guideline). They use IDR (Irreproducibility Discovery Rate), you can find some details here

https://sites.google.com/site/anshulkundaje/projects/idr

But it would be better to avoid MACS with IDR... You can use Macs.2 which seems to be ok
s.