stringtie output has exons instead of transcript annotation

[liux]

Hi,

has anyone used stringtie program? I have a genome annotation that mostly has one isoform annotated per gene. I tried to use stringtie to see if it can help get more transcript annotated. However openin the result GTF file in IGV I can only see individual exons. No transcripts whatsoever.

What is your experience? do I need to sepecify certain parameters to make it work?

Thanks!

[swaraj]

The output of StringTie should be in GTF format which reports Exons. The 9th column of the output contains name of transcript for each exon. If you visualise the GTF in IGV or some other genome browser you should be able to see the transcript models. Or to simplify you can convert your GTF into BED format using the script attached. The script requires BEDTools to be installed in your computer.