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Published 20 hours ago • verified publisher icon getzlab

rRNA counts differ

Open kray02 opened this issue 3 years ago • 3 comments

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

kray02 avatar Nov 06 '20 17:11 kray02

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.

francois-a avatar Nov 06 '20 19:11 francois-a

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

kray02 avatar Dec 04 '20 22:12 kray02

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

suzifei avatar Mar 04 '21 01:03 suzifei