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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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working with Integrated data #42

Closed AnjaliC4 closed 3 years ago

AnjaliC4 commented 3 years ago

Hi,

I integrated my data using harmony, but how do I do DA/TF motif/footprinting and others on the integrated data? I gave the path to integrated rds object but it seems like it needs path to an integrated filtered_matrix as well. Thanks!

wbaopaul commented 3 years ago

With the integrated seurat object, you can follow this tutorial to do some downstream analysis in R. For TF motif analysis, you need to output a matrix obj from that integrated seurat obj. The footprinting analysis, which needs merged bam files from different individuals, is not currently supported in scATAC-pro. I will probably add more downstrame analysis option for the integrated data for next update of scATAC-pro (like let the integrated obj be acceptable input for those DA/TF_motif analysis steps ). Thanks!

wbaopaul commented 3 years ago

I just realse version 1.3.0, which should be more friendly to the integrated data.

wbaopaul commented 3 years ago

I am closing this issue since no further response for more than 3 months.