I have some RNA-seq data from (human) cancer cells and am trying to find non-canonical transcripts (e.g. splice variants, fusion products, etc.). I have already created a SAM/BAM file of the transcripts and retrieved accession information (using MagicBLAST), but now what I'd like to do is filter out the "known" (canonical) transcripts and leave only the novel transcript variants. It seems like there should be an easy way to do this, but I'm at a loss as to where to find the a single collection of canonical transcripts to filter against....help?
Take all the Exon-exon junctions coordinates (i.e intron coordinates i.e retained introns) and check if they are in latest Gencode and FANTOM CAT GTF files. If not, pull out the transcripts that contain those junctions and create a new GTF file.
This will give you all novel transcripts that can have novel exon skipping/inclusion events and also alternate 3' and 5' splice sites.