ATAC-Seq Analysis - only peak counts and peak loci files available

Question

[gradovicheva]

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

[ATpoint]

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.

[RHI]

Hello all, I’m doing ATAC seq differential peak analysis. I only have a file with the peaks counts from 2 groups with 3 replicates each, and the peak loci in a bed file. I run the differential analysis using the peak counts file in DESeq2 and have a list of DE peaks. I would like to know how to annotate those regions to gene names using the peak loci in the bed file. From the peak count file I have a column with peak IDs in the format 1:181674-181967; while in the bed file I have 3 columns: chr number, start and end. How can I merge those files and identify the gene name annotations? Thank you so much!