PASA pipeline: compare experimental transcripts to the reference annotation
Answer from the authors: 


  PASA ends up using gff3 format instead of sam format for uploading the
  alignments.  If somebody has the gmap gff3 output, then can be done to
  just upload that directly using the custom alignment importer, but not
  with sam. They suggest just having PASA rerun GMAP as part of its
  regular routine.