Question: How to dump genes from GenBank in GFF3 format?
0
gravatar for Dan
21 months ago by
Dan500
Cambridge
Dan500 wrote:

If I look at this record in GenBank I see about 6k genes: https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts

I'd really like to be able to dump those genes in GFF3 format, but I'm guessing I can't do that in a single step, so...

  1. How to dump all genes from a GenBank record in 'whatever' format?
  2. How to convert 'whatever' format to GFF3?
genbank data-download gff3 • 829 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by Dan500
1

duplicate of Any tools converting Genbank format to GFF3 format?

ADD REPLYlink written 21 months ago by Pierre Lindenbaum118k
1

Hello Dan!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/853

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 21 months ago by Pierre Lindenbaum118k

Please limit cross-posting both here and on bioinformatics.stackexchange.com, it's a bit of a waste for people to reply in parallel at both places.

ADD REPLYlink written 21 months ago by Devon Ryan88k
0
gravatar for Dan
21 months ago by
Dan500
Cambridge
Dan500 wrote:

Ha, turns out you can just grab the GFF3 from the NCBI's FTP site!

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/195/GCA_000003195.3_Sorghum_bicolor_NCBIv3/

See:

Or "Access the data" on the right here:

ADD COMMENTlink written 21 months ago by Dan500
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