Question

Convert Gff3 (Augustus Output File) To Feature Table File (.Tbl) - Genbank Submit

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11.5 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 • 10k views

ADD COMMENT • link updated 6.3 years ago by arsilan324 ▴ 90 • written 11.5 years ago by elfeu ▴ 40

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Check this post on Seqanswers

ADD REPLY • link 11.5 years ago by Sukhi Singh 11k

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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!

ADD REPLY • link 11.4 years ago by Torst ▴ 980

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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

ADD REPLY • link 6.3 years ago by arsilan324 ▴ 90

score 1 · Answer 1 · 2017-06-26

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6.8 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

ADD COMMENT • link 6.8 years ago by Rahul Sharma ▴ 660

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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. :/

ADD REPLY • link 6.3 years ago by arsilan324 ▴ 90

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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?

ADD REPLY • link 6.2 years ago by arsilan324 ▴ 90