multiple-mappers ranking

[GoogleCodeExporter]

Hi,

I'd like to rank multiple-mappers based on the alignment quality.

following the manual, I can distinguish the secondary multi mappers from the 
primary

"For multi-mappers, all alignments except one are marked with 0x100 (secondary 
alignment) in the FLAG column 2. The un-marked alignment is either the best one 
(i.e. highest scoring), or is randomly selected from the alignments of equal 
quality."


is there a way I could rank the secondary multi mappers?


best,



M.

Original issue reported on code.google.com by [email protected] on 3 Feb 2014 at 6:17

[GoogleCodeExporter]

Please post your questions in the STAR forum 
https://groups.google.com/d/forum/rna-star for a faster reply.

The alignment score, recorded as AS attribute in the Aligned.out.sam file, can 
be used to rank the multiple alignments.

Original comment by [email protected] on 25 Feb 2014 at 10:29