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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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[request] implemantation of SEACR #951

Closed sunta3iouxos closed 9 months ago

sunta3iouxos commented 1 year ago

Hi again, is it possible to add the SEACR tool for cut&run analysis? Thank you. it appears that at the moment the de facto peak-caller for CUT&RUN (I am unsure on the CUT&TAG, since ATAC-seq optimised callers like Genrich could be better) is SEACR. The generated output is quite simple (bed format) and can be parsed to downstream analysis, like CSAW or motif analysis etc. The input requires bedgraph that is already produced from snakePipes.

Thank you EDIT: fixed grammar, for it to make sense.

katsikora commented 9 months ago

This is now available in snakePipes 2.8.0 and 2.8.1.