I have been running HISAT2 for some of my FASTQ files via
hisat2 -x genome --sp 1000,1000 -U /home/a.fastq.gz -S /home/output.sam
It worked and I got out:
16419826 reads; of these: 16419826 (100.00%) were unpaired; of these: 1719313 (10.47%) aligned 0 times 9510754 (57.92%) aligned exactly 1 time 5189759 (31.61%) aligned >1 times 89.53% overall alignment rate
However, when I looked into the data I found, that it was indeed 16419826 reads and 1719313 were not aligned, but it was 12448816 reads aligning exactly 1 time and 2251697 reads aligning more than 1 time.
Hence, the number I got out while looking at the data were a bit different.
How is that explicable? Did I do something wrong?
Many thanks for your help in advance!