I was hoping to use pizzly to identify fused genes im my Augustus gene predictions from a non-model organism.
I have an Augustus annotation of our critter and in principle the gene models look very nice, however we do know that there is a fraction of genes, which are fused, i.e. Augustus made a connection via a long(-ish) introns. I mapped extensive stranded RNA-Seq data we have against the Augustus predicted mRNAs (including the --fusin flag) with kallisto and thought I could then use pizzly to identify potential fusions, however now I am wondering how th gtf file you are asking for should look like? Is this congruent with a gff mapping the transcripts to the genome? Or should it be different, e.g. a per mRNA description of where exons and introns are in that specific sequence? Or am I getting all this completely wrong?
Hi there,
I was hoping to use pizzly to identify fused genes im my Augustus gene predictions from a non-model organism. I have an Augustus annotation of our critter and in principle the gene models look very nice, however we do know that there is a fraction of genes, which are fused, i.e. Augustus made a connection via a long(-ish) introns. I mapped extensive stranded RNA-Seq data we have against the Augustus predicted mRNAs (including the --fusin flag) with kallisto and thought I could then use pizzly to identify potential fusions, however now I am wondering how th gtf file you are asking for should look like? Is this congruent with a gff mapping the transcripts to the genome? Or should it be different, e.g. a per mRNA description of where exons and introns are in that specific sequence? Or am I getting all this completely wrong?
Thanks
Philipp