SAM primary FLAG from Tophat2

[loard]

Does anyone how Tophat2.0.11 chooses SAM primary (i.e. non 0x100) alignment? Is it the first in terms of coordinates, first depending on random seed of where to start aligning or else?



As I understand it:

-g sets the max number of reported alignments

In default mode, more between 1 and g alignments per read will be reported, only if all have the same, optimal score.

--report-secondary-alignment results in reporting some alignments with suboptimal score (Tophat "secondary"), if there is less than g alignments with optimal one.

Secondary 0x100 SAM flag is not what Tophat means by secondary - all suboptimal and all but one optimal alignment are "SAM secondary".

[vvv]

From the bowtie manual:

By default, bowtie2 searches for distinct, valid alignments for each read. When it finds a valid alignment, it continues looking for alignments that are nearly as good or better. The best alignment found is reported (randomly selected from among best if tied).