Chip Seq controls

Question

[wani.nisar]

Hello All,

I am presently working with breast cancer chip seq data housed in EBI for a variety of transcription factors. When I run MACS2 peak caller without control , I find some random peaks where are no where close to gene promoters.I was looking for control files for the experiments, but till now did not succeed.Any suggestions. Thanks in advance.

Answer 1

[Ian]

You could use blacklists from ENCODE/modENCODE to remove false peaks that overlap blacklisted coordinates.

Have you checked GEO or ArrayExpress to find input for the tissue you are investigating.