Gene Ids of type 'PRJEB28388_chrIII_pilon.g6753' are causing problems for the WS270 run of the gene descriptions pipeline ... Hinxton to make code change to remove the problem IDs from the production files.
It sounds like the reference will be updated soon.
The GFF File
The GFF also has some issues as well. For instance, I can't identify gene names in it via grepping:
In order to realign all strains, we’ll need to have a close look at the new genome.
I started to have a look at the new reference PRJEB28388 / VC2010. Here are some resources to start:
The reference
I downloaded the reference and the chromosome names look like this:
This is discussed in the minutes (linked above):
It sounds like the reference will be updated soon.
The GFF File
The GFF also has some issues as well. For instance, I can't identify gene names in it via grepping:
Additionally, the GFF contains a lot fewer annotations.
Other considerations
CeNDR has tracks for:
These are not easy to produce. Alternatively, we can try to lift them over to the new reference but that will definitely take some time.
How to obtain the reference
When this does get integrated, it should be done so using a script.