Same question was also posted here: https://github.com/infphilo/hisat2/issues/125
Briefly, when I was trying to extract unmapped reads from hisat2 results using
samtools -f 4. I got the alignment result like below:
HWI-ST845:121014:C17LHACXX:8:1101:10013:60438 69 19 37413559 0 * = 37413559 0 CCTCGGACCGCCCTTACAGCCATGCCCTGGTGGCTGGAATTGACCGCTAT CCCFFFFFHHHHHJJJJJJJJIJJJJJJJJFHJJJJJGHHIJIJHGDHHE YT:Z:UP
Does anybody know the reason? Thanks in advance.