Convert Gff3 (Augustus Output File) To Feature Table File (.Tbl) - Genbank Submit
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12.0 years ago
elfeu ▴ 40

Hello Guys,

I'm having a problem converting a gff3 file format (Augustus output file) in table feature table file (.tbl) to submit contigs in Genbank. Anyone have any script that does it?

Thanks!

gff3 • 11k views
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Check this post on Seqanswers

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Just be warned that you will still need to do a LOT of work to make the produced .TBL file have valid syntax and semantics for Genbank. It can be an exhausting process. Good luck!

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Hi Rahul,

The script you mentioned is producing genbank file format and not .tbl file. Can you please comment on it? Thanks

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7.3 years ago
Rahul Sharma ▴ 660

That could be done by using the EMBOSS seqret. Following are few examples:

For EMBL format conversion:

seqret -sequence test.fasta -feature -fformat gff -fopenfile test.gff -osformat embl -auto

For Genbank format conversion:

seqret -sequence test.fasta -feature -fformat gff -fopenfile test.gff -osformat genbank -auto

I hope this would be helpful.

Good luck

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This script is generating file which is never finishing and all your hard disc space in finished. I tried it on my pc first and then on external hard disc and 500 gb was not sufficient. :/

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I am trying to do this but its not working for me. It says after sometime "Killed: 9" Can you please comment?

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