macs2 callpeak -t Sort.Ref.G1.bam -c Ref.All_inputs.merged.subsampled.bam -n Macs.G1 --gsize hs --nomodel
the above gives 3000 peaks
macs2 callpeak -t Sort.Ref.G1.bam -c Ref.All_inputs.merged.subsampled.bam -n Macs.G1 --gsize hs
this one gives 1200 peaks.
I want to know, which is better or the correct way to call peaks, command 1 or command 2.
Could you please let me know.
Best regards
Abhishek
--
You received this message because you are subscribed to a topic in the Google Groups "MACS announcement" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/macs-announcement/VdH2agcGRX0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to macs-announcement+unsubscribe@googlegroups.com.
To post to this group, send email to macs-announcement@googlegroups.com.
Visit this group at https://groups.google.com/group/macs-announcement.
For more options, visit https://groups.google.com/d/optout.
Sounds like a good idea (assuming your fragment lengths were ~200 bp).It is also good practice to run the data through at least one other peak caller.
--