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How Interpret the hisat2 output?

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
ngs
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updated by Arup Ghosh Arup Ghosh • written by mathavanbioinfo mathavanbioinfo

1 answer

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.

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written by Arup Ghosh Arup Ghosh

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