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Question about parameter -uf
Hello, now I have a Nanopore cDNA sequencing data. And I detected the strands of every reads from the raw data. Then I mapped the reads to hg38 with minimap2 -ax splice -uf -t 8 $ref $reads >result.sam
. But the strand of some reads are not matched with my detection. For example, this is a read that detected as '-' : @100:1591|SRR25723945.21919894 9167ca31-862e-4ff7-900e-b2e4da99787b length=1668 strand=-
. But the mapping result reported it as a '+':
So which one should I choose from the 3 sets below? My data is neither a direct RNA nor an unknown strand data.