I have denovo assembled a genome. now I want to perform annotation on this.
I have tried maker-p but didn't get much success. any help from an expert is appreciable. We are open to collaborate as well.
which species are we talking here?
have you tried anything else than maker-p yet ?
I'm working on Moringa. plant.
I mainly tried maker-p. I found no other tool for plant annotation. (Braker required transcriptional data as well which I don't have).
Is that a new species or variety of this genus you sequenced?
Moringa (at least the oleifera) has been sequenced and annotated in the frame of the AOCC project. You can find that genome and it's annotation on ORCAE-AOCC
I have both oleifera and drouhardii.
depending on how quality you want the end result to be you can take the oleifera annotations/genes and blast those against the drouhardii genome (or vice versa), that should give you a good indication of the annotation.
that's what I did, except one or two genes nothing matched to that genome.
wait, so you took the oleifera genes/proteins and blasted those against the drouhardii genome and only one-two genes matched to it ?????
wow, that's quite unexpected :/ (are you sure all went technically OK?)
I checked the log and didn't found any error. All went ok..
I assume the drouhardii one is the one you want to annotate? (correct me if I'm wrong). and that one you assembled de-novo? How is that looking, I mean in assembly metrics, #contigs/Scaffolds, ... things like that?)
If that genome is hugely fragmented for instance I can see this happening.
Yes genome is highly fragmanted. The number of Contigs is quite high. I skipped contigs lower than 5000bp.
I see, would nonetheless be interesting to add some numbers here, so that we can see for ourself how it looks? What about N50 and such, median contig size ...
Number of contigs (after filtering ) = 36213
Total length = 2140007060
largest contig = 691164
N50 = 50133
OK, that's not brilliant but also not terribly poor . Should be good enough to annotate so the fact you can't find anything in that genome will not be caused by the assembly quality
what's the solution ?
for the moment: figure out why there is so little shared things between those two species, as this is something you would not expect from species within the same genus :/
Likely mean going back through your analysis and double check (and critically asses things)
ok.. what about other alternative to maker-p ???
what do you mean with "didn't get much success" ? it's not working technically? the result is poor (how do you know)? ...
I think both things.. It took forever to complete the annotation and then as I mentioned above except a few nothing matched to drouhardii genome. some were from humans some from other plants.
Try to do with augustus. Train augustus with the ORCAE-AOCC one and then use that training set for your genome.
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