minimap2 U to T conversion

Question

[kewoka9286]

Does minimap2 automatically convert U to T during the alignment process? I am seeing some conflicting information online, and wondering if this could be resulting in a very high amount of unaligned reads.

[GenoMax]

Are you asking about direct RNA sequencing using nanopore or for the reference being aligned to?

[kewoka9286]

The former

[WouterDeCoster]

I don't know, but wouldn't that be very easy to test? Create an artificial read, once with Ts and once with Us, and see how that is handled?

[GenoMax]

In limited testing minimap2 converts U calls in the read (I don't know if ONT direct RNA data has U's) when it does alignments. So it seems to work fine.