Does anyone know any packages that test to make sure ribosomal depletion took place? After illumina tru seq protocol

Question

[kcarey]

Are there any packages in R that does this? To check a bam file is not contaminated?

[andres.firrincieli]

There are faster methods to check the degree of rRNA contamination in your libraries. But if you really want to do this with R then, you can use Rsubread to count how many reads map to rRNA genes.

[cpad0112]

1. Index RNA sequences
2. Use fastqscreen on source fastqs (or from fastq obtained from bam - bam2fastq)

[kcarey]

Yes, I did this. Thanks I was wondering if there was a R package that did ribosomal contamination check. I wanted to create one.