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broad peak #207

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User-yx opened this issue Jan 18, 2021 · 1 comment

User-yx commented Jan 18, 2021

When I use macs2 call peak, can I set "--broad" parameters in this pipeline?

Contributor

leepc12 commented Jan 20, 2021

Currently there is no way to generate broad peaks.

Even if you edit https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/src/encode_task_macs2_chip.py#L86 to add --broad, pipeline will still try to find the narrowPeak file and will error out.

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