Extract rRNA from RNASeq data

[josh_OUS]

Hi everyone,
I'm new here and my searches didn't quite give me what I wanted so hopefully this isn't an already answered question. Any help is greatly appreciated.

I have some single end RNAseq data from a patient sample and I need to perform variant calling from specifically on the rRNAs. I would like to know what is the best method to extract the rRNA to perform the analysis. From what I have gathered, using STAR aligner and then using GATK tools to do the variant callings seems to be the best strategy.

Some background:
The original designers of the project hypothesise that there's potentially an error in the polymerase of the patient that causes error in the production of the rRNA. They have sequenced the total RNA but unfortunately, the sequencing company did their usual protocol and depleted the rRNA. But they suspect that there's at least some degree of rRNA left which can at least indicate if there's any indication for having variation in the rRNA sequences.

[GenoMax]

You can use the "filter" mode for "bbduk.sh" from BBMap suite for this. Download the human rDNA repeat sequence. Reads that match rDNA can be filtered away from your data. A guide to use bbduk is available here.

If most of rRNA has been depleted from your sample there is not much you can do.

[josh_OUS]

Thanks for the input! I'll look into this and see if I can salvage anything