tools to reconcile experimental transcripts with reference annotation Looking for tools to reconcile alignment file of experimental transcripts mapped to genome (SAM/BAM) with the reference transcriptome annotation (GTF) from Ensembl (organism: D. melanogaster). 

The aim would be to check which transcripts reported in the alignment file are also reported in the reference annotation, generating a new annotation (e.g., GTF) including the new transcripts as seen in the alignment file (experimental transcripts to genome).

Any idea?

-- Edit: 

Up to now, I tried an in-house script that does the following: 


generate a BED file from the BAM file with the exon coordinates (start/end) per transcript - using BEDOPS v2p4p27
convert the reference GTF to BED to retrieve the coordinates per annotated feature 
compare the experimental vs the reference BED intervals
infer the suite of annotated exons per experimental transcript, thus, ideally, the isoform it corresponds to


However, with this simple approach, I only get around 20% of the experimental transcripts that can be identified in all their length using reference annotation. This might be due either to a too simple approach (e.g. if the start/end of the exon in the experimental transcript is shifted by 1 base as compared to the reference, it won't be detected), or to a real biological signal (since I am also using data from long-read sequencing technologies).
I've never tried this myself, so I don't know how easy this is...

One option would be to start with GMAP, which is meant to align whole transcripts against the genome. The really nice thing about this is that it can directly produce GFF3 files. You can then use that with your Ensembl GTF with cuffcompare or whatever the equivalent is in stringTie. You should then be able to get the information you want from the transfrag codes.