Recently I am trying to call differential peaks using DEseq2. I have got ATAC-seq data for 10 samples (5 time points and each time point has 2 replicates). Here is the workflow I trying to establish:
1) Call peaks using MACS2
2) Count the number of reads for each peak in each sample separately using featureCounts (Rsubread package). The output matrix is as follow.
3) Merge 10 read counts matrices
sample1 sample2 sample3……
peak_1 100 94
peak_2 178 243
4) Feed the merge matrix to DEseq2
However, I encounter a trouble when I am trying to merge these 10 matrices Because the rownames of each matrix is different. Some of them represent the same or similar location of the chromosome but using different peak id. I am wondering what's the best way to solve this problem. I will appreciate any hits! Thanks!