Entering edit mode
7.9 years ago
Nicolas Rosewick
11k
Hi,
I aligned some paired-end reads on hg19 and found some strange stuff (at least for me..). Some reads have NH:i:1 i.e. the read aligned in one position and XT:A:R i.e. XT:A:R flag indicates that the second read is repetitive. I don't understand how reads that align to one position (NH:i:1) can be repetive .. or maybe I'm missing something ?
Here's an example for a pair of reads :
M00991:78:000000000-AP8FW:1:1101:3646:9757 1:N:0:59 99 chr11 7381659 3 83M = 7381659 83 TAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACTCATGAGCATGGAATGTTCTTCCATTTGTTTGT HHHHHHHHGHHHGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHGHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHH XT:A:R NM:i:0 AM:i:3 NH:i:1
M00991:78:000000000-AP8FW:1:1101:3646:9757 1:N:0:59 147 chr11 7381659 3 83M = 7381659 -83 TAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACTCATGAGCATGGAATGTTCTTCCATTTGTTTGT HHHHHHGGHHHHHHHHHHHHHHHHGHHGHHHGHHHHHHHHHGHGHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHH XT:A:R NM:i:0 AM:i:3 NH:i
NH is the number of reported alignments, not possible alignments. So it will never be greater than 1 unless you are reporting secondary alignments.
Could you please explain the difference between reported alignment and possible alignment?
Many thanks!
Tagging: Brian Bushnell