I am new to the ATAC and I am not sure how to analyze it. how to calculate ATAC-Seq cut sites for each peak from ATAC data??
I use featureCounts using the --read2pos 5 option to only count the 5' end of each read (so of both R1 and R2 since each 5' end is a cutting site). That assumes you are asking how to make a count matrix, but your question is actually unclear. Please be more precise what you actually want to do.
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