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

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

annotation embl
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updated by GenoMax GenoMax • written by robert.murphy • robert.murphy

1 answer

There are two CDS because there are two isoforms

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written by Juke34 Juke34

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

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written by robert.murphy • robert.murphy

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

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written by Juke34 Juke34

You can accept the parent answer to provide closure to this thread.

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written by GenoMax GenoMax

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