Question: Does Chromvar require bulk ATAC-seq?
0
gravatar for jmah
3 months ago by
jmah10
jmah10 wrote:

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!

atac-seq scatac-seq chromvar • 183 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by jmah10
1

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 REPLYlink written 3 months ago by ATpoint31k

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.

ADD REPLYlink written 3 months ago by jmah10

erased and rephrased original q

ADD REPLYlink modified 3 months ago • written 3 months ago by jmah10
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