text: user294: I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation.
  In more detail, I am working with RNA-seq data from D. melanogaster. I have reconstructed the 'transcripts' using Trinity. I have aligned these 'transcripts' to the reference genome using GMAP. Now I would like to match these 'experimental transcripts' with the reference annotation, to see how they compare.
  I was wondering if I can run just a subset of the whole PASA pipeline, so basically skipping the step of alignment to the reference and using the alignment file that I generated externally.
  Also, I would be glad to receive more general redirecting to any released software allowing the comparison of experimental transcripts to the reference annotation. 
  Cross-posted on the PASA Google Group pasapipeline-users
  Cross-posted on biostars
  
  user294: 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.
  
  
original_text: 294: <p>I would like to ask if anyone has experience in running a subset of the <a href="https://github.com/PASApipeline/PASApipeline/wiki" rel="nofollow noreferrer">PASA pipeline</a>, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation.</p>
  
  <p>In more detail, I am working with RNA-seq data from <em>D. melanogaster</em>. I have reconstructed the 'transcripts' using Trinity. I have aligned these 'transcripts' to the reference genome using GMAP. Now I would like to match these 'experimental transcripts' with the reference annotation, to see how they compare.</p>
  
  <p>I was wondering if I can run just a subset of the whole PASA pipeline, so basically skipping the step of alignment to the reference and using the alignment file that I generated externally.</p>
  
  <p>Also, I would be glad to receive more general redirecting to any released software allowing the comparison of experimental transcripts to the reference annotation. </p>
  
  <p>Cross-posted on the <a href="https://groups.google.com/forum/#!topic/pasapipeline-users/cyG9e8-HjG8" rel="nofollow noreferrer">PASA Google Group pasapipeline-users</a></p>
  
  <p>Cross-posted <a href="https://www.biostars.org/p/260594/" rel="nofollow noreferrer">on biostars</a></p>
   294: <p><a href="https://groups.google.com/d/msg/pasapipeline-users/cyG9e8-HjG8/jSwb9o4kAAAJ" rel="nofollow noreferrer">Answer from the authors</a>: </p>
  
  <blockquote>
    <p>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.</p>
  </blockquote>
  