rRNA counts differ

[kray02]

Is there any equivalent to the legacy version -BWArRNA using bwa to count rRNA reads? That seems to be a more accurate option.

[francois-a]

We did not find this to be substantially different for assessing sample quality, and removed this option in v2 for simplicity. Please make sure rRNA intervals are properly defined in the GTF annotation you're using.

[kray02]

We had a batch of RNAseq where the rRNA depletion kit failed. This shows the samples with the most/least rRNA (and a few in the middle). v2 does not detect this issue.

comparison.txt

[suzifei]

Hi,
Most publicly available GTFs (Ensembl for example) do not have well-defined rRNA intervals in their GTFs. This is why the BWA method using a fasta of rRNA sequences is superior. Do you have a straightforward suggestion for how to obtain well-defined rRNA intervals for a variety of species to append to our chosen GTFs?
Thanks,
Suzi