pure Biochemistry lab want to do ATAC-seq?

[翁靖傑]

Dear all,

I am in a pure biochemistry lab. We want to use ATAC-seq to analyze the whole genome chromosomal open/close in response to my treatments. However, we found it not easy. Even though we can finish the library construction and sequencing in our institute, the bioinformatic center is not experienced in ATAC-seq analysis. I found NYU and Cornell provided the ATAC-seq. Does anyone cooperate with them? Is there any other way for a pure biochemistry lab to do this kind of analysis easier?

Welcome any suggestion.

Thaks!!

JJ  

[Hunter Richards]

There is nothing special about ATAC-seq that would require a different analytical pipeline that is any different than how you would process ChIP-seq data. The ATAC-seq paper used ZINBA, but others use MACS and presumably the peak-caller of choice for the given lab/researcher.

Align with Bowtie (or your favorite aligner) then call peaks with MACS or QuEST (my suggestion since they're easy to use). I don't think it even requires an input control since it's not a ChIP.

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Hunter Richards

Project Scientist

Department of Genome Dynamics
Lawrence Berkeley National Laboratory
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