Question: Differential Binding in Partek
0
gravatar for DVA
19 months ago by
DVA540
United States
DVA540 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 • 495 views
ADD COMMENTlink modified 19 months ago by kgosche20 • written 19 months ago by DVA540
0
gravatar for kgosche
19 months ago by
kgosche20
kgosche20 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 19 months ago • written 19 months ago by kgosche20

Commercial product, be aware.

ADD REPLYlink written 13 months ago by ATpoint38k
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