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elkebir-group / doubletD

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shallow scATAC-seq data? #3

Open Urja25 opened 1 year ago

Urja25 commented 1 year ago

Can this platform be used for shallow scATAC-seq data? I have output from cellranger atac count pipeline. How can I generate doubletD inputs from this?

lweber21 commented 1 year ago

Unfortunately, I don't think this will work for shall scATAC-seq data as it models the read counts at each SNV locus. I'm not too familiar with cellranger atac count pipeline. Are you able to obtain variant and total read counts for a set of loci? If so, what is the average coverage at each locus?