MACS3 in pipeline - Githubissues

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

http://snakepipes.readthedocs.io

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MACS3 in pipeline #1019

Closed sunta3iouxos closed 1 month ago

sunta3iouxos commented 3 months ago

Hi all, is MACS3 implemented/substitute MACS2? Apart from any improvements MACS3 incorporates HMMRATAC that is a better alternative for ATAC-seq peak calling.

Thank you

katsikora commented 2 months ago

Hi,

we don't have MACS3 implementation as yet.

Best wishes,

Katarzyna

katsikora commented 2 months ago

HMMRATAC is already available in the ATAC-seq workflow via --peakCaller HMMRATAC .