Question: How Interpret the hisat2 output?
gravatar for mathavanbioinfo
10 days ago by
mathavanbioinfo10 wrote:

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 • 83 views
ADD COMMENTlink modified 10 days ago by arup1.5k • written 10 days ago by mathavanbioinfo10

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

ADD REPLYlink written 10 days ago by lakhujanivijay4.2k
gravatar for arup
10 days ago by
arup1.5k wrote:

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.

ADD COMMENTlink written 10 days ago by arup1.5k
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