[Gmod-help] Re: [Gmod-gbrowse] Configure Gbrowse

Kris T ktruncali at gmail.com
Thu Jul 30 16:28:28 EDT 2009


I think the tables are basically just tab delimited text files.

Here is an example:
#ID_REF =
#VALUE = number of times sequenced
ID_REF    VALUE
AAAAAAAAAAAAAAAAAAGCTCAAAAAAAAAACAAC    2
AAAAAAAAAAAAAAAAAAGGCTAAAAAAAAAAAAAA    1
AAAAAAAAAAAAAAAAAATCTGAAAAAAAAAAAAAA    10
AAAAAAAAAAAAAAAAAATGGGCCCCAAGAAAAAAA    1
AAAAAAAAAAAAAAAAACACCGAAAAAAAAACAAAA    1
AAAAAAAAAAAAAAAAACACTCGAAAAAAAAAAAAA    1
AAAAAAAAAAAAAAAAACGATGATGTAAAAAAAAAA    1
AAAAAAAAAAAAAAAAAGCTCAAAAAAAAAAAAAAA    4
AAAAAAAAAAAAAAAAATGAGGAAATAAAAAAGAAA    5
AAAAAAAAAAAAAAAAATTGACAAAAAAAAAAAAAA    4
AAAAAAAAAAAAAAAACACCACAAAAAACCAAAACA    2
AAAAAAAAAAAAAAAACACCCAAAACAAAAAAAACA    4
AAAAAAAAAAAAAAAACAGATTTTTACAAAAAAAAA    1
AAAAAAAAAAAAAAAACCCAACCCCCACCATAAAAA    1
AAAAAAAAAAAAAAAACCCACAACAAAAAAAAAAAA    2
AAAAAAAAAAAAAAAACCCACGCCAAAAAAAAAAAA    1
AAAAAAAAAAAAAAAACCGTATCCCGTAAAAAAAAA    1
AAAAAAAAAAAAAAAAGAACTTAACCAAAAAAAAAA    1
AAAAAAAAAAAAAAAAGCCCAAAAAAAAAAAAAAAA    3
AAAAAAAAAAAAAAAAGGAAGGCCCAAAAAAAAAAA    2
AAAAAAAAAAAAAAAAGTCTGAAAAGAAAAAAAAAA    2
AAAAAAAAAAAAAAAATCAATCAATTTAAAAAAAAA    9
AAAAAAAAAAAAAAAATCCAACGAAAAAAAAAAAAA    2
AAAAAAAAAAAAAAAATGAGCAAAAAAAAAAAAAAA    4
AAAAAAAAAAAAAAAATGCCGAAAAAAAAAAAAAAA    25

Thanks,
Kris


On Wed, Jul 29, 2009 at 5:36 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Kris,
>
> I apologize for the very slow response.  It has been (and will
> continue to be) a very busy 2 months for GMOD.
>
> What does your .txt file look like?  Can you include and example here?
>  You may have to write your own script to translate it into GFF3
> (http://gmod.org/wiki/GFF3), or if it's in a widely used format, you
> may be able to use an existing script.
>
> Thanks,
>
> Dave C.
>
> On Mon, Jul 20, 2009 at 9:40 AM, Kris T<ktruncali at gmail.com> wrote:
> > Hi everyone,
> >
> > I got Gbrowse installed and running. Thanks for all your help.
> >
> > Now, I want to configure Gbrowse to work with our database. However, the
> > database files are in txt format (not .gb format). I don't see a way to
> get
> > them in .gb format. Is there some way I can still configure Gbrowse to
> work
> > with our tables?
> >
> > If I pasted the text in the .txt file over the contents of a .gb file,
> would
> > that be a usuable data source for Gbrowse?
> >
> > Thanks,
> > Kris
> >
> >
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