PASA pipeline: just compare to the reference annotation

[Amina Echchiki]

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.

Best,
Amina

[Brian Haas]

Hi Amina,

PASA ends up using gff3 format instead of sam format for uploading the alignments.  If you had the gmap gff3 output, you could just upload that directly using the custom alignment importer, but not with sam.

I'd suggest just having PASA rerun GMAP as part of its regular routine.

best,

~brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas