Hisat-3N mapping quality

[ZiggeyQi]

Hi, there

I use Hisat-3N to align my paired SLAMseq data (trimmed), everything works OK, but i find the reads mapping quality of the output SAM file just contain the value 0, 1, 60, does it normal or something wrong with my data. My SLAMseq is total RNAseq instead the 3'-RNAseq, i uesd the repeat-index and the splicing-site-aware model for indexing (info were provided by hisat2_extract_splice_sites.py and hisat2_extract_exons.py) , also the --repeat for alignment. Should i filter my read by the mapping quality threshold 20, or some advices to me. Your reply is highly anticipated.

Best,
Ziggey