How Interpret the hisat2 output?

Question

[mathavanbioinfo]

hi, I got hisat( Human sample hg38) the first line says 59.74 percentage aligned 0 times, is these results are reliable!!!!

2423323 (59.74%) aligned 0 times
        1430953 (35.27%) aligned exactly 1 time
        202462 (4.99%) aligned >1 times
93.60% overall alignment rate

[lakhujanivijay]

Check this Too low mapping percentage using HISAT2 on human reference genome.

Answer 1

[Arup Ghosh]

The number of unaligned reads is very high in your dataset. Generally, 10-15% of unaligned reads will not impact downstream analysis but in this case, you will lose a large subset of transcripts as the aligned reads will be mostly dominated by highly abundant transcripts if you don't have more replicates with better alignment rate.