Question: Check an abinitio annotation from Augustus
gravatar for Roxane Boyer
3.1 years ago by
Roxane Boyer1.0k
France / Toulouse / GeT-Plage
Roxane Boyer1.0k wrote:

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.



annotation genome • 1.1k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 3.1 years ago by Roxane Boyer1.0k
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