How to extract GFF

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

How to extract GFF

David Octavio Botero Rozo
To extract all the GFF, on console type this two commands:

mkdir gff
find foldernameofGFF --name *.gff --exec cp {} gff \;


This copy all the GFF to a new folder "gff"

--
David Octavio Botero Rozo

Biologist
System Engineering Student
Associated Researcher - CENICAFE
Colombia

Tel: +57-685056550 ext. 317-338
Cel: +57-3214719269

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: How to extract GFF

Carson Hinton Holt
Re: [maker-devel] How to extract GFF Also for creating a combined GFF3 (useful when loading data into Chado) there is a script that come with MAKER

gff3_merge gff/*.gff #if you’ve already copied all GFF3 files into another directory
gff3_merge –d genome.maker.output/genome_master_datastore_index.log #if you want to let gff3_merge find the data in the MAKER output

Be aware that copying all GFF3 files into a single directory can overload the directory structure if there were more than 32,000 contigs in the input fasta file to the MAKER job as each contig will create it’s own GFF3.  You can also turn off the MAKER’s datastore function by using the option –nodatastore if traversing the directory structure becomes annoying.

Carson


On 10/11/10 10:03 AM, "David Octavio Botero Rozo" <doboteror@...> wrote:

To extract all the GFF, on console type this two commands:

mkdir gff
find foldernameofGFF --name *.gff --exec cp {} gff \;


This copy all the GFF to a new folder "gff"

--
David Octavio Botero Rozo

Biologist
System Engineering Student
Associated Researcher - CENICAFE
Colombia

Tel: +57-685056550 ext. 317-338
Cel: +57-3214719269


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org