Question: ATAC-Seq Analysis - only peak counts and peak loci files available
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3 months ago by
gradovicheva0 wrote:

I have a file with peak counts (2 groups - treated and control, 3 replicates each) and a bed file with peak loci. I don't have access to any prior files i.e. fastq and BAM files, so cannot complete the full workflow from scratch. Could anyone advise on how I could perform differential accessibility analysis only with this data?

Thank you

sequencing chip-seq • 223 views
ADD COMMENTlink written 3 months ago by gradovicheva0

With peak counts I assume a count matrix with rows = peak regions of both conditions and columns = the raw counts for every sample? If so, you can feed that into any downstream franework you like, e.g. edgeR, DESeq2.

ADD REPLYlink modified 3 months ago • written 3 months ago by ATpoint14k
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