Why chromosome coordinates were given for unmapped reads in hisat2?

Question

[xieshaojun0621]

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.

[xieshaojun0621]

I think you are right.

Here are the alignment information for both reads:

HWI-ST845:121014:C17LHACXX:8:1101:10013:60438   137 19  37413559    60  50M =   37413559    0   GTTGACAACAGTCTTGTCCAAGGGGATATCCACAGAGTACCTTGTGGGCA  CB@FFFFFHHHHHJJJJJJJJJJJJGIIJIJJJJJJJFGHIJJJHIIJJD  AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UP NH:i:1

HWI-ST845:121014:C17LHACXX:8:1101:10013:60438   69  19  37413559    0   *   =   37413559    0   CCTCGGACCGCCCTTACAGCCATGCCCTGGTGGCTGGAATTGACCGCTAT  CCCFFFFFHHHHHJJJJJJJJIJJJJJJJJFHJJJJJGHHIJIJHGDHHE  YT:Z:UP

Thank you for the quick response.

Answer 1

[swbarnes2]

Why don't you check the mapping coordinate of the mate? Some aligners will give an unmapped read the same coordinates as its mate, so they stay together when sorted by position in the bam.