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Old 04-16-2014, 11:57 AM   #5
tnp
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Location: Denmark

Join Date: Nov 2008
Posts: 1
Default bam tags AS and XS

A comment to how uniquely mapped reads can be extracted. As far as I understand a read is uniquely mapped when AS and XS tags differ - pls correct me if im wrong. Actually I have seen XS values being bigger than AS values which I dont really understand - Cant find a thorough description of what XS orhter than its the score for a suboptimal alignment.

ex with XS bigger than AS:
HWUSI-EAS664L:24:64FGCAAXX:4:11:3337:6807 99 gi|407955691|dbj|AP012495.1| 1359455 0 101M = 1359704 351 CCAATGGCCGCTGCCAGTGGCGTTTTGTCGTGTCTTTCCGGGTTGGACTCAAGTTGATAGTTACCGGA
TAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTC IIHGDIIIIGIIDIIIIEHIIIIGIIGHIIIIHHHIIIIIHIEIIIHIIIHGHIIIFGHIFIHHHIICIGHHHIIIBCGHGEGHGGDGHBEGGIGEFEAD? NM:i:8 MD:Z:3G4T13A1A0A10A16A0C46 AS:i:62 XS:i:68

So is this an example of a uniquely mapped read ?
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