SeqMonk rRNA from QCplot 100%

Question

[ED]

Dear all,

I have single-end RNAseq data that I mapped with Hisat2 and am looking at in SeqMonk. I plotted the QC plot (default) + Measure rRNA. I got 100 % rRNA. Which I think is impossible right? Or did I do something horribly wrong in the mapping?

Thank you in advance.

Answer 1

[ED]

I actually think I found the answer, but I am not sure. Apparently, the .gtf file has no annotation for rRNA (just CDS, exon, gene, stop_codon, start_codon). So there is no mapping to rRNA ... and I think SeqMonk does not deal with that? Maybe someone can correct me or tell me what someone would normally do here.

Thanks again.