Gff3 - moving an annotation from scaffold level to pseudomolecule level

Question

[Philipp Bayer]

I have an annotation for a genome assembly in scaffold format in gff3/fasta format - someone else has ordered these scaffolds into pseudomolecules, so now I want to move the 'old' annotation in gff3 format from their scaffold positions into the pseudomolecules' position.

I could write a script to do this but I'm sure I'll introduce off-by-one errors everywhere. Is there any package out there which takes two gff3 files (gene positions on scaffolds, and scaffold positions in pseudo-molecules) and generates a new annotation gff3 with the gene positions on pseudomolecules?

Answer 1

[kfletcher]

Would recommend flo https://github.com/wurmlab/flo

It doesn't do exactly as you request. From memory, flo instead aligns the two assemblies and produces a new GFF file on the second assembly.

One thing, the gene lines have to be removed from the GFF file. They provide a script to do so. I don't think they provide a script to put the gene lines back in.

Answer 2

[Carambakaracho]

Hi Philipp, might liftOver do what you want?

Though my impression is that data prep might just take as long as writing the script.