Question: MACS2 with multiple replicates
0
gravatar for ariel.balter
19 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 • 2.0k views
ADD COMMENTlink modified 5 months ago by Hmd10 • written 19 months ago by ariel.balter130
1
gravatar for Praneet Chaturvedi
19 months ago by
Cincinnati Children's Hospital and Medical Center
Praneet Chaturvedi100 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 19 months ago by Praneet Chaturvedi100

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

ADD REPLYlink written 19 months ago by ariel.balter130
0
gravatar for James Ashmore
19 months ago by
James Ashmore2.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.5k wrote:

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

ADD COMMENTlink modified 19 months ago • written 19 months ago by James Ashmore2.5k

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

ADD REPLYlink written 19 months ago by ariel.balter130
0
gravatar for Hmd
5 months ago by
Hmd10
Hmd10 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 5 months ago • written 5 months ago by Hmd10
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