minimap’s SAM file MAPQ value for the unique alignments

minimap’s SAM file MAPQ value for the unique alignments

0

Hi,

I have mapped my reads from nanopore RNAseq to the reference database using the minimap. Minimap SAM files have MAPQ values from 0 to 60 in the fifth column. While 0 indicates the reads that can possibly map to many locations and have the lowest quality, 60 indicates the highest quality and unique reads.

I am losing a bit more reads at the MAPQ 60 and the reads are way shorter (up to 200-300bp, I want at least 1000bp). I was wondering what could be the minimum MAPQ values that I can use to retain the unique reads with better length and quality.

Thanks a lot.


minimap


MAPQ


RNAseq

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