I want to calculate RPKM of ATAC-Seq data but I do not find any script for that. As I am new to bioinformatics, so would be grateful if somebody guide me.
This is what you're looking for.
Check out this very famous tool DeepTools.
But deeptools produce graph and I need values of RPKM
cisDynet can help you analyse ATAC-seq data!
I suggest you make a Tool post to highlight what your tool can do rather than adding unrelated answers to existing threads.
The simplest would be to read the matrix of raw counts into R, and use something like edgeR::rpkm(). See edgeR documentation. You would need to provide the region length to edgeR for RPKM, otherwise CPM would do well, so no length correction.
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