what does uT tags stand for?

[Peng]

Hi,

In STAR's output bam file, I observed lines with uT tags. I think they are used for labeling unmapped reads, but not sure what's the difference between uT:A:0, uT:A:1, uT:A:2, and uT:A:3. I guess they may represent 'too short', 'too many mismatches', 'mapped to too many loci'. Could some one help to clarify that? Thank you.

I have searched this group, STAR's manual, and googled around, but didn't find any affirmative answer to it. Sorry if I missed anything.

Best,

Peng  

  

[Alexander Dobin]

Hi Peng,

they indeed mark "unmapped Type", 0="other" (no good anchor seeds), 1='too short', 2='too many mismatches', 3='mapped to too many loci'.

Cheers

Alex

[Peng]

Thank you, Alex! It is very helpful.

Best,

Peng