Why does RNA sequencing data has Thymine as opposed to Uracil? Theoretically, it shouldn't be.

Question

[Shaurya Jauhari]

As per definition, RNA has a quarternary composition of A,C,U,G. The RNA- sequencing data that is outputted from the next generation sequencing experiments still holds a T (from DNA) and not U. Why does the Uracil base has to be disengaged here?

Answer 1

[mark.ziemann]

Because sequencing occurs after conversion to double stranded complementary DNA (wikipedia). Some systems like Oxford Nanopore are the exception because they read RNA directly ONT website.

[Emily]

Making this something of a philosophical discussion: should the sequence reported be what we believe to be the sequence of the molecule (ie Uracil) or should it be what actually comes out of the sequencing machine (ie Thymine)? Which answer is more accurate?

[WouterDeCoster]

In my opinion what we call "RNA-sequencing" is not RNA sequencing but cDNA sequencing, and therefore it's a T.

When sequencing RNA directly (Oxford Nanopore) the output is a U. Note that this is a problem for aligners ;-)

[Kristoffer Vitting-Seerup]

I think Its much more useull to have it as T since that allows direct mapping to the genome

[WouterDeCoster]

Aligners never had to keep U into account, but I guess that's something that's going to change in the very near future.