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wbaopaul / scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
MIT License
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peak calling macs2 for c. elegans #8

Closed lengfei5 closed 4 years ago

lengfei5 commented 4 years ago

Hi,

Thank you for such a flexible and nice processing pipeline. I went though the source code and found that the peak calling, macs2, the organism parameter is only for human and mouse. So I am wondering if possible to put this parameter for macs2 into configuration_user file. Perhaps together with macs other parameters, e.g. --nomodel --extsize 147, because macs2 complained without those parameters.

Thanks.

lengfei5 commented 4 years ago

I realized that people can easily add more parameters for macs2 in configuration_user file. Then please ignore then extra pamameters, eg. --nomodel --extsize 147. Please only move the organism parameter into the configuration_user.

wbaopaul commented 4 years ago

Good point! I just updated it as you suggested, thanks.

Wenbao