Differential Binding in Partek

Question

[DVA]

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!

Answer 1

[kgosche]

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.

[ATpoint]

Commercial product, be aware.