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!
1 answer
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.
Log in to answer this question.
-
Question about constructing a consensus peak file for diffTF
written by lilithslily •
-
Overestimate of ATAC-seq differential peaks
written by Darryl •
-
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
written by cyril-cros
-
Differential Peak Analysis from ENCODE Pipeline normalized outputs
written by sjquon •
-
Differential binding ChIP-seq/RNA-seq analysis
written by dcheng1 •
-
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
written by a.rex
-
Normalization and differential analysis in ATAC-seq data
written by anais1396 •
-
Diffbind - Very high proportion of significant peaks
written by kautilya
-
peaks overlap: ATAC & CHIP seq
written by sophialovechan •
-
Compromise null hypothesis when calling differential binding between ChIP-seq conditions
written by James Ashmore
