Question about Minimap2 and nanopore reads

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Hi,

I was wondering if Minimap2 is able to align reads that are the flipped reverse complement of the reference? After analyzing my reads, I have found sample barcode sequences in the normal 5’-3’ sense, but also in the flipped reverse compliment sense. This must be due to the fact that the nanopores can accept either end of the cDNA strand. So does Minimap2 take into account these flipped RC sequences when aligning reads to a reference sequence?

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Hi @scca
Maybe check it. Select a single read, create a reverse complement sequence and align both to the reference. Check the results.
Aligners map reads in both orientations, and expect no issue with RC reads.
Kind regards,
Igor