Help in using GBrowser for my academic project.

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Help in using GBrowser for my academic project.

Latha Battu
Dear Sir,

I am B. Latha an M.Tech student doing my academic project in Bioinformatics using GBrowser. I am facing  little  difficulty in using GBrowser. I am working on genome wide analysis of rice genome for multiple promoters  containing  genes. I got my partial results and converted it into GFF2 Format.

Sir please help me with following doubts:

1. How to upload my GFF2 format data into GBrowser ( if possible help me with youtube links)

2. How to upload through custom tracks and get results of chromosomes showing locations of multiple promoters containing genes.


Thanking you,


Latha Battu.

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Re: Help in using GBrowser for my academic project.

Scott Cain
Hi Latha,

I don't know of any YouTube links for this sorry.  Can you please tell us what instance of GBrowse you are using (the URL) and provide a sample of the GFF you've created?  Also, is there a reason you're using GFF2 rather than GFF3?  I find GFF3 easier to understand in most cases.

Scott



On Sat, Nov 9, 2013 at 9:20 AM, Latha Battu <[hidden email]> wrote:
Dear Sir,

I am B. Latha an M.Tech student doing my academic project in Bioinformatics using GBrowser. I am facing  little  difficulty in using GBrowser. I am working on genome wide analysis of rice genome for multiple promoters  containing  genes. I got my partial results and converted it into GFF2 Format.

Sir please help me with following doubts:

1. How to upload my GFF2 format data into GBrowser ( if possible help me with youtube links)

2. How to upload through custom tracks and get results of chromosomes showing locations of multiple promoters containing genes.


Thanking you,


Latha Battu.

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Help in using GBrowser for my academic project.

Scott Cain
Hi Latha,

Please keep the GBrowse mailing cc'ed in you responses. 

This is the support mailing list for people who have installed and maintain a copy of the GBrowse software; we'd like to help you too, but you haven't told us where the GBrowse instance you're referring to is.  Is it something you or a coworker installed, or is it available on the internet somewhere?

Also, I'd point out that what you sent in your attachment was not a GFF file but a Microsoft Excel file.  You could probably turn this into a GFF file fairly easily by saving as a tab delimited text file, though you should make sure to add a space between "promoter_id" and the id in the ninth column.

Scott



On Wed, Nov 13, 2013 at 2:34 AM, Latha Battu <[hidden email]> wrote:
Dear Sir,

Firstly thank you so much for the reply.I am sending you the GFF2 files that i have created by using Molquest tool of Softbery. My work requires GFF2 rather than GFF3. Sir, I am using Genome browser for the first time, my GFF2 Files contains the information of the genes in rice having multiple promoters, to show the locations of this multiple promoter on the chromosomes diagramatically i am using GBrowser. Showing the location of multiple promoters on each chromosome is the final step of my project please help me in uploading this GFF2 files into the GBrowser and getting results. I am sending you the attachments. Please help me sir.

Thank you,

Latha Battu


On Wed, Nov 13, 2013 at 9:44 AM, Scott Cain <[hidden email]> wrote:
Hi Latha,

I don't know of any YouTube links for this sorry.  Can you please tell us what instance of GBrowse you are using (the URL) and provide a sample of the GFF you've created?  Also, is there a reason you're using GFF2 rather than GFF3?  I find GFF3 easier to understand in most cases.

Scott



On Sat, Nov 9, 2013 at 9:20 AM, Latha Battu <[hidden email]> wrote:
Dear Sir,

I am B. Latha an M.Tech student doing my academic project in Bioinformatics using GBrowser. I am facing  little  difficulty in using GBrowser. I am working on genome wide analysis of rice genome for multiple promoters  containing  genes. I got my partial results and converted it into GFF2 Format.

Sir please help me with following doubts:

1. How to upload my GFF2 format data into GBrowser ( if possible help me with youtube links)

2. How to upload through custom tracks and get results of chromosomes showing locations of multiple promoters containing genes.


Thanking you,


Latha Battu.

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
Free app hosting. Or install the open source package on any LAMP server.
Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
_______________________________________________
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