No peaks detected in chipseq analysis-macs3

Question

[bioinfo_ga]

Hi .. I am doing peak analysis using macs3 for ralstonia samples with the below command for paired end data:

macs3 callpeak -t t.bed -c c.bed --outdir ../Peak/c --nomodel -q 0.01

i tried inc the q value still do not get any peaks what could be the reason?

Thanks

[ATpoint]

The most obvious reason is (please do not feel offended, it's not meant to be mocking you) that there are no peaks. Have you checked data on the IGV? Make a bigwig track, e.g. using bamCoverage from deeptools, and just "look" at the data.

[Darked89]

Side issue: MACS3 can accept BAM as an input: MACS3 docs so there is no need to create often giant BED files from BAMs