I have been converting IsoSeq long reads from a fasta file to GFF/GTF formats using exonerate. I have been using the default parameters and the est2genome option in client serve mode. Everything ran and worked great, but the final GFF is missing ~2000 of the original 17000 transcripts. I was just wondering if anyone has experience using exonerate, and can offer any reason why this might be happening. I imagine that these 2000 transcripts do not have matches based on the default thresholds, but I haven't been able to find any evidence of this in the exonerate user manual.
Thank you Harry