Does Chromvar require bulk ATAC-seq?

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4.4 years ago

jmah ▴ 20

According to the Chromvar vignette (https://bioconductor.org/packages/release/bioc/vignettes/chromVAR/inst/doc/Introduction.html), "If analyzing single cell data, it can make sense to use peaks derived from bulk ATAC-seq". The wording is confusing. Do they mean use annotation of peaks defined by bulk ATAC-seq as the 'reference' against which to align single cell ATAC-seq reads? Why can't we use a consensus peak set derived from the single cell data instead?

I've read the methods section of the Nature Methods paper (https://www.nature.com/articles/nmeth.4401#Sec3) and I'm still a little unclear on this.

Thanks for your help!

scATAC-seq ATAC-seq Chromvar • 1.5k views

ADD COMMENT • link 4.4 years ago by jmah ▴ 20

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I guess they mean that you should use bulk peaks to create the count matrix that chromVAR analyzes as bulk has higher coverage and therefore creates more reliable peaks.

ADD REPLY • link 4.4 years ago by ATpoint 82k

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Thank you! That makes a lot of sense. I'm very new to this (if that wasn't obvious) and I really appreciate your help.