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.