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Hi ATpoinrt,
Thank you!
I saw this in the results generated by a software called flair (https://doi.org/10.1038/s41467-020-15171-6)
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When you say "extract the haplotypes", are you referring to the read alignments themselves, or do you mean inferring the underlying haploty…
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Looks like a job for [bioawk][1]. For example, if you just need the IDs (like in the seqkit answer above), you can do this:
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#name %unambiguousReads unambiguousMB %ambiguousReads ambiguousMB unambiguousReads ambiguousReads assignedReads assignedBases
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Align to the hairpins, not the mature miRNA file. This should get you started preparing a `hsa` hairpin file.
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