Question about rRNA in data

Question

[joerodger2017]

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

Answer 1

[Carlo Yague]

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.

[A. Domingues]

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?

[Carlo Yague]

Oh yes, you are right. In fact, I meant that

You can't quantify rRNA directly using FASTQC

[WouterDeCoster]

Would be best to edit your post to clarify what you actually meant.