Question: Genbank To Gtf Converter
3
gravatar for Leszek
8.8 years ago by
Leszek4.1k
IIMCB, Poland
Leszek4.1k wrote:

Are you aware of any gb2gtf converter?

ADD COMMENTlink modified 5.5 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Leszek4.1k
7
gravatar for Leszek
8.8 years ago by
Leszek4.1k
IIMCB, Poland
Leszek4.1k wrote:

I have written naive gb2gtf converter. You can find it here.
Let me know if you have any comments.

ADD COMMENTlink written 8.8 years ago by Leszek4.1k

Thanks for the script! I needed a gtf file to use with RSEM and this worked wonderfully. The code is nicely annotated so that I could modify as needed.

ADD REPLYlink written 3.7 years ago by fa2570
0
gravatar for Damian Kao
8.8 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

BioPerl does have a [?]bp_genbank2gff.pl[?]

You can then convert the GFF to GTF. I am not sure if there is any standardize tool that can do that because GFF can be kinda vague with its formatting. You can use BioPerl again to parse the GFF and convert it to the correct [?]GTF format[?].

ADD COMMENTlink written 8.8 years ago by Damian Kao15k
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