Hi everyone !
I'm having trouble again with my genome annotation project. I'm trying to de novo assemble and then annotate the D. suzukii genome, which is a closely related species from D. melanogaster.
Beside maker, I wanted to use Augustus at first in order to have a glance at how an abinitio tool, without any hints file, will work on my genome assembly.
I succeed to produce a first gff3 file, made by Augustus, which look like this :
tig00000001 AUGUSTUS gene 1 4045 0.02 - . ID=g1 tig00000001 AUGUSTUS transcript 1 4045 0.02 - . ID=g1.t1;Parent=g1 tig00000001 AUGUSTUS intron 1 21 0.95 - . Parent=g1.t1 tig00000001 AUGUSTUS CDS 22 482 0.95 - 0 ID=g1.t1.cds;Parent=g1.t1 tig00000001 AUGUSTUS exon 22 647 . - . Parent=g1.t1 tig00000001 AUGUSTUS start_codon 480 482 . - 0
I could visualize my gff3 track on IGV with my assembly, but the gene are not "identified" (gt.t1, ect).
So I was asking myself how could I "compare" my results to something else, (D; melanogaster genome ? previous D; suzukii assembly ?), how can I "identify" each gene ? (for example, what could be more likely the predicted gene g1.t1 ? Is it Orco ? is it Yellow ?)
Sorry if I'm being unclear, I'm still a bit confused with all the different steps, as it's my first time having such a long project all by myself.
Thanks for helping me ! I'll try to clarify if I was really unclear.