Question: less significant summits were called, but more significant ones were neglected (macs2 callpeak -t myfile.bed -f BED --nomodel extsize 10 -q 0.02 --call-summits)

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wendy

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Jun 4, 2018, 5:24:32 PM6/4/18

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Dear you who could help,

I have a bed file in which all the reads are with fixed length of 10.

To call summits, the command I used was,

macs2 callpeak -t myfile.bed -f BED --nomodel extsize 10 -q 0.02 --call-summits

Generally the summits are right.

However, as shown in the image here:

My question are: Why the left two summits, which actually were lower than the nearby regions, got called? Why the highest pileup was not called? Do you have any suggestions to optimise my command ?