rRNA Contamination checks?

[apeltzer]

Hi!

just because it came up recently: One could indeed use RSEQC to check with a given BED file for rRNA contamination / incomplete depletion of rRNA using a BED file of such positions. That could serve as an additional QC / optional step... any thoughts on this?

Would only require adding these BED files for rRNA positions on the respective genomes I guess and using the script provided by RSEQC already...

[drpatelh]

I think we need to decide which QC software we are going to use first - RseqC or Qualimap or both. You can extract ribosomal intervals from the gtf file using biotype on the fly and then feed that to a downstream QC tool in the required format. I do that with RNASeqC and it works quite well.

[ewels]

That would be super nice! Especially fetching the intervals automatically.. Might need to add support to MultiQC 🙄

[d4straub]

If there would be not only an rRNA check but even a rRNA depletion process, maybe by e.g. SortMeRNA against a 16S database such as SILVA than this pipeline might also work for environmental metatranscriptomics.