Macs2 failed for pooled samples

Question

[GR]

Dear All,

I am new to ChIP analysis. I have 3 replicates for ChIP samples and 2 for control samples. I am using macs2 for peak calling. It was all going well until I called peaks on pooled replicates.

MACS2 command:

macs2 callpeak -t chipdata_pooled.tagAlign.gz -c mocksamples.tagAlign.gz -f BED -n chipdata_pooled_VS_mocksamples -g 1.1e8 -p 1e-3

I get the following error and the program terminates:

Too few paired peaks (91) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.

I did not get the above issue with the individual replicates. Can anyone please help.

Many thanks,

Answer 1

[EagleEye]

Hi,

I have a suggestion. Instead of pooling the samples, I would recommend calling peaks for individual replicates and use IDR.

[GR]

I am very confused now. I actually started following IDR pipeline. Does not it recommend to run macs2 on both individual replicates and pooled replicates? https://sites.google.com/site/anshulkundaje/projects/idr