Question: MACS2 with multiple replicates
0
gravatar for ariel.balter
13 months ago by
ariel.balter130
ariel.balter130 wrote:

When you use macs2 with multiple replicates is it just pooling the replicates or doing something more sophisticated?

chip-seq macs2 • 1.1k views
ADD COMMENTlink modified 13 months ago by James Ashmore2.3k • written 13 months ago by ariel.balter130
1
gravatar for Praneet Chaturvedi
13 months ago by
Cincinnati Children's Hospital and Medical Center
Praneet Chaturvedi40 wrote:

You can use ENCODE IDR pipeline with peak caller as MACS2 to call peaks which are reproducible across replicates. Here is the link : https://sites.google.com/site/anshulkundaje/projects/idr

Cheers !!

Praneet

ADD COMMENTlink written 13 months ago by Praneet Chaturvedi40

I just want to know what method macs2 is using. Calling multiple replicates with macs2 is part of the encode pipeline.

ADD REPLYlink written 13 months ago by ariel.balter130
0
gravatar for James Ashmore
13 months ago by
James Ashmore2.3k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.3k wrote:

As far as I'm aware it just pools the replicates.

ADD COMMENTlink modified 13 months ago • written 13 months ago by James Ashmore2.3k

Yeah I think you are probably correct based on the output I got.

ADD REPLYlink written 13 months ago by ariel.balter130
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