Comments (3)
I wasn't able to reproduce this issue with the latest version of HISAT2 using my own test set and your example reads. Please let me know if you have some examples for which HISAT2 reports identical alignments.
from hisat2.
@infphilo what version is that?
from hisat2.
@infphilo hi. what version???
from hisat2.
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from hisat2.