twoPassMode --Basic: will junctions inserted on the fly be considered annotated?

[Ryan Englander]

Hi Dr. Dobin,

I am wondering if, when running twoPassMode --Basic, whether novel unannotated junctions that are inserted into genome indices on-the-fly will be considered annotated for the final output. Thanks so much!

Kindest regards,

Ryan Englander

[Alexander Dobin]

Hi Ryan,

that's correct; the novel junctions from the 1st pass inserted in the genome for the 2nd pass, will be considered annotated in the 2nd pass, in addition to the "true" annotated junctions from GTF.