minimap's SAM file MAPQ value for the unique alignments

Question

[Mo]

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.

[GenoMax]

Look at the distribution of MAPQ values and decide. See: https://github.com/lh3/minimap2/issues/447

[WouterDeCoster]

It always depends on what you want to do with the data.

to the reference database

That is not too specific, do you mean genome, transcriptome, or something else?

[Mo]

Hi, I am sequencing RNA of the GFP library, so I am mapping to GFP sequences (database having 5'UTR-CDS-barcodes_3'UTR of all the variants).