[Gmod-ajax] A couple of questions (relative coordinates, multiple projects)

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[Gmod-ajax] A couple of questions (relative coordinates, multiple projects)

David Breimann
Hello,

1. I'm trying to figure out how to use relative coordinates in a GFF
file under JBrowse.
Let's say I have I have a chromosome (chr1) of size 5Mbp. I loaded its
sequence and annotations to JBrowse.
Now I would like to focus on a specific region withing this chromosome
(region1) of 100kb - let's say chr1:100001-200000, and use a GFF file
(region1.gff) with coordinate relative to region1 (e.g. a feature in
region.gff with coordinates 1 100 will be displayed on chr1
100001-100100).
Is this possible?

2.I would like to have multiple JBrowse projects, each in a separate
folder. I tried the --out options of the bin scripts bu then when I
browsed to localhost/jbrowse I ended up with a blank age. Where should
I point my browser?

Thanks,
David

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Re: A couple of questions (relative coordinates, multiple projects)

Dave Clements, GMOD Help Desk-3
Hi David,

It looks like your GFF3 was answered (negatively) on the GBrowse list.  

Did you resolve your second question yet, or is it still an open problem?

Thanks,

Dave C

On Sat, Jul 3, 2010 at 6:05 AM, David Breimann <[hidden email]> wrote:
Hello,

1. I'm trying to figure out how to use relative coordinates in a GFF
file under JBrowse.
Let's say I have I have a chromosome (chr1) of size 5Mbp. I loaded its
sequence and annotations to JBrowse.
Now I would like to focus on a specific region withing this chromosome
(region1) of 100kb - let's say chr1:100001-200000, and use a GFF file
(region1.gff) with coordinate relative to region1 (e.g. a feature in
region.gff with coordinates 1 100 will be displayed on chr1
100001-100100).
Is this possible?

2.I would like to have multiple JBrowse projects, each in a separate
folder. I tried the --out options of the bin scripts bu then when I
browsed to localhost/jbrowse I ended up with a blank age. Where should
I point my browser?

Thanks,
David

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