which one is best for motif discobery in human paired-ends chip-seq?

[yueli]

Hello,

I am working on human paired-ends chip-seq data analysis.

Which software or web tools is the best for motif discovery?

Thanks in advance!

With Best!

Yue

[atpoint]

findMotifs.pl from Homer and MEME-ChIP from the MEME suite are the two most popular. Check out both and then choose the one you feel more comfortable with. I typically use homer as it is quiet intuituive to use.

[yueli]

atpoint,

Thank you so much for your great help!