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!