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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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macs2 q-value #206

Open User-yx opened 3 years ago

User-yx commented 3 years ago

When I use macs2 call peak, can I set the q-value instead of the p-value in this pipeline?

leepc12 commented 3 years ago

https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/chip.wdl#L990

Edit this line in chip.wdl.

                        else if peak_caller_=='macs2' then 'q.value'