Question: MACS2 with multiple replicates
0
gravatar for ariel.balter
6 weeks ago by
ariel.balter70
ariel.balter70 wrote:

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

chip-seq macs2 • 178 views
ADD COMMENTlink modified 6 weeks ago by James Ashmore1.5k • written 6 weeks ago by ariel.balter70
1
gravatar for praneet007
6 weeks ago by
praneet00730
praneet00730 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 6 weeks ago by praneet00730

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

ADD REPLYlink written 6 weeks ago by ariel.balter70
0
gravatar for James Ashmore
6 weeks ago by
James Ashmore1.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore1.5k wrote:

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

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by James Ashmore1.5k

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

ADD REPLYlink written 5 weeks ago by ariel.balter70
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