minimap2 U to T conversion
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.
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GenoMax
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kewoka9286 •
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kewoka9286 •
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Are you asking about direct RNA sequencing using nanopore or for the reference being aligned to?
The former
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?
In limited testing
minimap2convertsUcalls 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.