I have a question about one of discussion @ Cleaning RNA-Seq data from rRNA How can be quantify rRNA in FASTqC I dont see any parameter, Yes we can see poly A tails in over-repsesnted seq. It just refer to % of over-represented seq or there is another way of FASTqc showing rRNA contamination.
Thanks
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joerodger2017 •
Hi,
You can't quantify rRNA directly in fastqc, but sometimes, if you take the overrepresented sequences and blast them against a database containing the transcriptome of your organism, you will find that those sequences come from rRNAs. So it is not a quantification, it just tells you that you have a lot of rRNA in your library.
If you need a quantification, you will have to map your reads agains genome or transcriptome.
You can't quantify rRNA directly
Can't it be done by mapping to rRNA sequences or counting those mapping to annotated rRNA in the genome?
Oh yes, you are right. In fact, I meant that
You can't quantify rRNA directly using FASTQC
Would be best to edit your post to clarify what you actually meant.
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