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No peaks detected in chipseq analysis-macs3

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

chipseq
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updated by Darked89 Darked89 • written by bioinfo_ga • bioinfo_ga

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.

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written by ATpoint ATpoint

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

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written by Darked89 Darked89

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