How to generate bigwig file of defined subset of nuclei?

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

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How to generate bigwig file of defined subset of nuclei? #133

Open wulabupenn opened 4 years ago

wulabupenn commented 4 years ago

Hi Rongxin,

SnapATAC is an awesome package for single cell ATAC-seq analysis. After peak calling by MACS2, I am wondering how can I generate the bdg or bigwig file of a subset of nuclei based on combined peaks.

Thanks, Peng

r3fang commented 4 years ago

Hello,

Thank you for your nice comments. After running MACS2, it should automatically generate a bdg file in the current folder. If not, you can set tmp.folder="./" to current folder.