[Gmod-help] Gmod sequence data for build36?

[Scott Cain]

Hi John,

I don't know off hand of a source of human GFF3 files, though I
imagine they exist.  I did find this email about converting UCSC mysql
tables to GFF3:

  https://stat.ethz.ch/pipermail/bioconductor/2005-August/010011.html

though that is getting pretty old by now; I have no idea if this
works.  There is also the ucsc_genes2gff.pl script that is distributed
with GBrowse but it is fairly limited in terms of what you get out
(just IDs and coordinates, I believe).

For more information and suggestions, I would suggest that you send an
email to the GBrowse mailing list, as there are many subscribers and
it is entirely likely that someone there knows better where to get the
GFF3 files you're looking for.  See this page for subscribing
information:

  https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Scott




On Mon, Aug 4, 2008 at 8:18 PM, John Major <John_Major at perlegen.com> wrote:
> Hello-
>
>
>
> I see there are directions for loading sequence data in GMOD, but I am
> having a hard time figuring out how to do this.
>
> We have a current GMOD install(1.69).
>
>
>
> If I want to load sequence data for chromosomes 1-22, X, Y, is there a
> build36 GFF3 file set?
>
>
>
> I'm not entirely clear what these need to look like(ie- what id's do these
> files need to link to, if any).
>
>
>
> Do I need just one GFF3 file per chromosome, then use bp_bulk_load_gff.pl?
>
>
>
> Thanks!
>
> John



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory