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?
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Shaurya Jauhari •
1 answer
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.
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 ;-)
I think Its much more useull to have it as T since that allows direct mapping to the genome
Aligners never had to keep U into account, but I guess that's something that's going to change in the very near future.
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