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 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.