peak calling from chip seq data

[Ranjita Thapa]

Hello Dr. Fidel,

I have a question on peak call using deeptools. I am doing peak call from chip seq data. I do have a peak calls output using MACS2 tool. I want to estimate the peak coverage statistics for upstream region, downstream region and gene body for all the genes (>30,000).

I am wondering if deeptools could handle this. I would appreciate your suggestion.

Thanks

Ranjita

[Devon Ryan]

You can do this by creating a bigWig from the macs peaks (use 1 for
regions where there's a peak and 0 otherwise) and then using that as
normal. In general we think it's more useful to use bigWig files made
from BAM files, since you get the most out of your data then.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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