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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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MAPQ score query #108

Open prasundutta87 opened 7 years ago

prasundutta87 commented 7 years ago

Hi,

Can you please give more details about mapq scores? I only got three unique score 0,1 and 60. As most other aligners, the highest score is usually given to the uniquely mapped read. Can you please conform that and give more information about the scoring scheme? My analysis depends on this information.

jduc commented 6 years ago

Hey, yes please, if you could add some explanation it would be very useful.

From what I understand, mapQ of 60 is the max, it should indicate uniquely mapped read. Is it possible to have a mapQ of 60 but an NH flag different than 1 ? And what is the diff between mapQ 1 and mapQ 0? Also, this issue is similar than this one: issues/88 Thank you very much for your help.