blasr SAM output tags

[Aizon]

Hello,

Would love it if someone could clarify a couple of things concerning the tags in the SAM file from BLASR.

1) What do the YS and YE represent? Fairly sure they are start and end coordinates but, of what?

2) XQ is supposed to be the query sequence length, but where does it come from? I am trying to understand an inconsistency between the XQ value, and the subread coordinates. For example, how can a subread "movie/zmw/0_3904" have XQ:i:3984 ?

Thanks

[Aizon]

Bump!
Anyone?

[rhall]

You may want to also post to:
https://github.com/PacificBiosciences/blasr/issues

[Aizon]

Dear rhall,

frankly, if you don't have the answer, that makes me lose hope!

On a more serious note, I am guess the XQ might be the length of the polymerase read, but it would be nice to have a confirmation. Will try my luck, as you suggested, in https://github.com/PacificBiosciences/blasr/issues

[rhall]

The specifics for the exact method of indexing alignments and subreads always confuses me, I just about understand it for raw blasr output, but without reading the code I have no idea when it comes to SAM output. The Blasr developers tend to respond to issues on github.

[Aizon]

They indeed were quite fast to reply!

I'm posting their reply here, if anyone comes up with the same questions, here is the answer:

(1) YS and YE are start and end position of query subread in the coordinate of zmw unrolled polymerase read.

(2) XQ is length of zmw unrolled polymerase read.

The Wiki of Blasr sam output format has been updated. Please let me know if the description is still misleading. Thanks!

Yuan

Source: https://github.com/PacificBioscience...mment-94974442