Question: Gff3 - moving an annotation from scaffold level to pseudomolecule level
gravatar for Philipp Bayer
12 days ago by
Philipp Bayer5.9k
Philipp Bayer5.9k wrote:

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?

annotation assembly • 127 views
ADD COMMENTlink modified 11 days ago by Carambakaracho760 • written 12 days ago by Philipp Bayer5.9k
gravatar for kfletcher
11 days ago by
kfletcher10 wrote:

Would recommend 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.

ADD COMMENTlink written 11 days ago by kfletcher10
gravatar for Carambakaracho
11 days ago by
Carambakaracho760 wrote:

Hi Philipp, might liftOver do what you want?

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

ADD COMMENTlink written 11 days ago by Carambakaracho760
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