Question: Convert Gff3 (Augustus Output File) To Feature Table File (.Tbl) - Genbank Submit
2
gravatar for elfeu
7.0 years ago by
elfeu40
elfeu40 wrote:

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 • 6.5k views
ADD COMMENTlink modified 21 months ago by arsilan32470 • written 7.0 years ago by elfeu40
2

Check this post on Seqanswers

ADD REPLYlink written 7.0 years ago by Sukhdeep Singh9.9k
1

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 REPLYlink written 6.9 years ago by Torst950

Hi Rahul,

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

ADD REPLYlink written 21 months ago by arsilan32470
1
gravatar for Rahul Sharma
2.3 years ago by
Rahul Sharma600
Germany
Rahul Sharma600 wrote:

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 COMMENTlink written 2.3 years ago by Rahul Sharma600

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 REPLYlink modified 21 months ago • written 21 months ago by arsilan32470

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

ADD REPLYlink written 20 months ago by arsilan32470
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