Question: Differential Binding in Partek
0
gravatar for DVA
10 weeks ago by
DVA510
United States
DVA510 wrote:

Hello,

Does anyone have a protocol or recommended pipeline for doing differential peak/binding analysis in Partek. I want to compare ATAC-seq results from two different conditions, but a ChIP-seq based pipeline would also be useful.

Diffbind and csaw seem good but these are not available in Partek. EdgeR and DEseq2 are available, but to use these I would need some way to turn MACS2 called peaks into features before I can use them. Any advice please?

Thank you very much!

atac-seq chip-seq partek • 136 views
ADD COMMENTlink modified 10 weeks ago by kgosche0 • written 10 weeks ago by DVA510
0
gravatar for kgosche
10 weeks ago by
kgosche0
kgosche0 wrote:

You can perform that analysis fully within Partek Flow. Run the Quantify Regions tool on the Peaks data node (output of MACS2) and the result (Quantification Result data node) will give you number of reads per region. You can then proceed to DESeq2 or another statistical tool.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by kgosche0
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