SeqMonk rRNA from QCplot 100%
1
0
Entering edit mode
7 weeks ago
ED • 0

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 • 179 views
ADD COMMENT
0
Entering edit mode
7 weeks ago
ED • 0

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2444 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6