contig to scaffolds annotations

[migrau]

Hi all,
I am a bit confused about the 'conversion' of contigs to scaffolds.
I have contigs.fasta & contigs.gff files and I generated a scaffolds.fasta but now, I don't know how to use the old gff file:

contig00001     maker   gene    147643  150477  .       -       .       ID=...
contig00001     maker   mRNA    147643  150477  .       -       .       ID=....
...

because it is related with the contigs.

How can I obtain a scaffolds.gff file?

Thank you!

[Brian Bushnell]

You can't simply 'convert' contigs to scaffolds; they have to be assembled using additional data.

Anyway, to get a new gff file, use the same annotation process that was used to generate the gff from the contigs. If you don't know how that was done, I recommend sticking with the contigs and not doing scaffolding.

[Wallysb01]

If you ran maker on just the contigs of your genome assembly and now you have scaffolds, you should rerun maker from the beginning on those scaffolds. Trying some sort of liftover of your gff file is certainly possible, but the annotation will be much worse than something run on the presumably much superior assembly using scaffolding information.