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

Question

[elfeu]

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!

[Sukhi Singh]

Check this post on Seqanswers

[Torst]

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!

[arsilan324]

Hi Rahul,

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

Answer 1

[Rahul Sharma]

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

[arsilan324]

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. :/

[arsilan324]

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