ATAC-Seq and RPKM

Question

[qudrat.nii]

Hi,

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.

[Yogi]

This is what you're looking for.

Check out this very famous tool DeepTools.

https://deeptools.readthedocs.io/en/2.4.0/content/tools/bamCoverage.html

[qudrat.nii]

But deeptools produce graph and I need values of RPKM

[Tao Zhu]

cisDynet can help you analyse ATAC-seq data!

[ATpoint]

I suggest you make a Tool post to highlight what your tool can do rather than adding unrelated answers to existing threads.

Answer 1

[ATpoint]

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.