Our lab are working on alternative splicing event in some non-model organisms
however, there are few mRNA (transcripts) in the annotation files, 1 transcript per gene in most cases. We thought that it is because the genome is poor annotated, so we collect a lot RNA-seq data and apply Hisat and StringTie to generate novel splice variants There are a lot more transcripts, reaching 2 transcript per gene in the output
However, we concern about the new transcripts, as the new transcripts exceed the gene region in the annotation file, in some case the whole exon exceed the gene region, and a few cases the whole transcript exceed the gene region..
May i have your advice on other tools or what do you think about the new transcripts? do you think they are acceptable? is there any handy tool to find new combination of exon from RNA-seq data and .gtf annotation file? thank you very much!!