All GFF features placed on each scaffold in multi-FastA file

[kubu4]

I have a multi-FastA file containing 18 genomic scaffolds. I also have a GFF containing gene features for all of the scaffolds. However, Artemis appears to be mapping all gene features to each and every scaffold.

The screencap below shows:

• Green box highlights different scaffold names in the gene GFF

• Red arrow shows Artemis currently viewing "Scaffold_01"

• Green arrows show gene GFF coordinates from different scaffolds are listed in the Artemis Scaffold_01 features list, even though only one of the gene features actually belongs in Scaffold_01

Any thoughts on what is happening here and/or how to correct this?

[tseemann]

Wow - that error used to happen years ago when you used a Genbank reference. But it works with GFF 3.0 normally.

Did you run art ref.fa + ref.gff ?

One idea might be to make a single GFF file as follows:

echo "##gff-version 3" > fixed.gff
cat ref.gff >> fixed.gff
echo "##FASTA" >> fixed.gff
cat ref.fa >> fixed.gff

and try loading that