Question: MACS2 with multiple replicates
0
gravatar for ariel.balter
2.5 years ago by
ariel.balter140
ariel.balter140 wrote:

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

chip-seq macs2 • 3.6k views
ADD COMMENTlink modified 16 months ago by Hmd40 • written 2.5 years ago by ariel.balter140
3
gravatar for Hmd
16 months ago by
Hmd40
Hmd40 wrote:

Pooling replicates could not be sophisticated, as it does not account for differences across replicates. Instead use either of the followings:

  • call peaks on each of the replicates separately using MACS, then process the replicates using MSPC, which keeps only reproducible peaks (combines p-values and then applies a threshold on their right-tail probability) and generates a set of "consensus" peaks.
  • use comparative peak callers such as jMOSAiCS, which is specifically developed to call peaks considering multiple replicates.
  • last option could be IDR, AFAIK it does not account for replicate type and does not consider strong peaks as "reproducible" if are not overlapping with other peaks. This is a problem with Bio replicates specifically, because there is a degree of discrepancy between the bio reps (as opposed to tech reps). BTW, MSPC "confirms" strong peaks in bio reps even if they do not overlap with any other peak (this is a configurable as you can adjust it with its c parameter).
ADD COMMENTlink modified 16 months ago • written 16 months ago by Hmd40
1
gravatar for Praneet Chaturvedi
2.5 years ago by
Cincinnati Children's Hospital and Medical Center
Praneet Chaturvedi120 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 2.5 years ago by Praneet Chaturvedi120

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

ADD REPLYlink written 2.5 years ago by ariel.balter140
1
gravatar for James Ashmore
2.5 years ago by
James Ashmore2.7k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.7k wrote:

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

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by James Ashmore2.7k

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

ADD REPLYlink written 2.5 years ago by ariel.balter140
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