ATAC-Seq and RPKM
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4 months ago
qudrat.nii ▴ 10

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.

RPKM ATAC-Seq • 861 views
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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

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But deeptools produce graph and I need values of RPKM

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cisDynet can help you analyse ATAC-seq data!

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

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4 months ago
ATpoint 80k

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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