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.