If there any output file about peak calling

aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data

MIT License

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If there any output file about peak calling #33

Closed werhoog closed 6 years ago

werhoog commented 6 years ago

Hi， I have use this software well . However , I can't find any files out abut peaks since I use .bam file to call peak with MACS2. Can I obtain it by some extra parameter?

caleblareau commented 6 years ago

Yes, you can retain these using the --keep-temp-files flag. I may try to make this more clean though.

caleblareau commented 6 years ago

@werhoog in the newest version of hichipper v0.7.2 (just pushed to PyPi), a {SAMPLE}.anchors.bed file is now output per-sample as a default.

also requested by @sowmyaiyer