gene body coverage with RSeqQC

Question

[wiscoyogi]

I'd like to visualize the gene body coverage and I wanted to use RSeqQC given that it's an established tool.

I downloaded the directory directly off the site (RSeQC-5.0.1) however it's failing for qcmodule import from qcmodule import getBamFiles ModuleNotFoundError: No module named 'qcmodule'

I'm confused because these import lines in the script are commented as #import my own modules but there is no directory or script called qcmodule in the entire downloaded directory that I can find with grep.

Would be greatful for any/all guidance for (1) how to get this package to work (2) alternate means to reliably visualize gene body coverage

thanks!

Answer 1

[BioinfGuru]

Take a look at this post ... it might give a clue.

Alternatively, for my installation the qcmodule is located at:

/home/bioinfguru/micromamba/envs/rseqc/lib/python3.8/site-packages/qcmodule

I install rseqc with micromamba and have never had any issues.