PASA pipeline: just compare to the reference annotation

Question

[dovah]

Hello,

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 'transcipts' 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 bam file that I generated externally.

Many thanks in advance.

cross-posted: https://groups.google.com/forum/#!topic/pasapipeline-users/cyG9e8-HjG8

[Devon Ryan]

Hello dovah!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/969/pasa-pipeline-compare-experimental-transcripts-to-the-reference-annotation

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[dovah]

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.