Remove rRNA for RNA-Seq Analysis

Question

[Saran]

Hello,

I am performing RNA-Seq analysis on 6 samples (3 infected & 3 control). I aligned my samples to GENCODE's release 41 primary assembly and quantified my fragments using RSubread::featurecounts(). So now I have a counts matrix and have TMM normalized my counts in EdgeR. I removed genes that are lowly expressed and would like to remove Ribosomal genes.

I am thinking that I could just remove rows in my matrix that correspond to the 62 genes classified as Ribosomal at HGNC's website : https://www.genenames.org/data/genegroup/#!/group/1379. Is this an effective method of removing ribosomal rna counts from my analysis?

Thank You, Sara

[acvill]

You'll want to remove reads mapping to rRNA before normalizing with EdgeR.

[Saran]

Yes, that is true, I will re-run normalization when I figure out how to remove rRNA genes.

Answer 1

[Mensur Dlakic]

In my experience, this is a most reliable way of detecting rRNA sequences:

https://github.com/hzi-bifo/RiboDetector

[GenoMax]

Curious is this program works for normal RNAseq samples. Page indicates that it is for metagenomeic, metatranscriptomic, and ncRNA sequencing data.