How to solve multiple CDS features with same locus tag in EMBL format

Question

[robert.murphy]

I have generated some EMBL files from gff3 format and am ending up with multiple CDS features at the same locus tag. From the ones I have checked, it is 2 CDS features per locus tag. Is this because there is one CDS on the forward strand and one on the reserves strand?

The tool I am wanting to use does not allow for multiple CDS on the same locus tag so how can I avoid this happening or a simple way to change it automatically?

Example EMBL: https://pastebin.com/LkzfB0nF

Answer 1

[Juke34]

There are two CDS because there are two isoforms

[robert.murphy]

Is there a way I can avoid this? Or at least give different locus tags. I want to use antiSMASH and it does not allow multiple CDS at one locus tag

[Juke34]

Prior conversion you can use AGAT to keep only longest isoforms.

[robert.murphy]

This have solved the issue, thank you!

[GenoMax]

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