SeqMonk rRNA from QCplot 100% · Biostar

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SeqMonk rRNA from QCplot 100%

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.

RNAseq QC from Seqmonk

rrna rnaseq seqmonk

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written 4.7 years ago by ED •

1 answer

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.

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written 4.7 years ago by ED •

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