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Re: tutorial

Aravind PRASAD

Hi Scott,

 

Thank you for the tutorial link. I have got a solution to represent the features in different colours.

 

Regards,

Aravind.

 

From: Eric Yao [mailto:[hidden email]]
Sent: Tuesday, 11 April, 2017 11:56 AM
To: Scott Cain
Cc: JBrowse List
Subject: Re: [Gmod-ajax] Not able to call jbrowse in browser

 

oh, very nice, scott!

 

On Mon, Apr 10, 2017 at 2:27 PM, Scott Cain <[hidden email]> wrote:

Hi Ajay,

 

There is also this tutorial that I sometimes give:

 

 

It tries to go into a little more depth on some topics, like changing how the track looks.

 

Scott

 

 

On Mon, Apr 10, 2017 at 4:08 PM, Eric Yao <[hidden email]> wrote:

Hi Ajay,

 

This is the detailed reference for configuration options for your tracks (in trackList.json):

http://gmod.org/wiki/JBrowse_Configuration_Guide#Feature_Tracks_.28HTMLFeatures_and_CanvasFeatures.29

 

This configuration in your track config determines whether you are using either CanvasFeatures viewer or HTMLFeatures viewer.

"type": "JBrowse/View/Track/HTMLFeatures",

 

 

On Mon, Apr 10, 2017 at 12:54 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

 

I have finished the tutorial.

And now able to run jbrowse with my own data set..

But I could not understand how I can change viewing pattern of the track also color of track. Like white  to red. Or blue

Please help me as I am very much new to this domain.

 

Waitimg.for your kind response.

Thanks and Warm Regards

Ajay

 

On Apr 11, 2017 1:18 AM, "Eric Yao" <[hidden email]> wrote:

Hi Ajay,

A good place to start is here:

The example shows how to import your gff file among other.

 

 

 

 

On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

 

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

 

There are also desktop versions you can try:

 

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

 

 

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

 

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

 

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

 

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

 

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

 

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

 

Waiting for your reply and suggestion to solve this problem.

 

 

Thanks and Warm Regards

 

 

--

Ajay Kumar Mahato
(Research Associate)

 

ISCB Indo-Swiss collaboration in Biotechnology

National Research Centre on Plant Biotechnology
(www.nrcpb.org)
Indian Agricultural Research Institute, Pusa Campus
New- Delhi -110012

Contact No. <a href="tel:&#43;91%2098683%2003571" target="_blank">+91- 9868303571

 

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--

Ajay Kumar Mahato
(Research Associate)

 

ISCB Indo-Swiss collaboration in Biotechnology

National Research Centre on Plant Biotechnology
(www.nrcpb.org)
Indian Agricultural Research Institute, Pusa Campus
New- Delhi -110012

Contact No. <a href="tel:&#43;91%2098683%2003571" target="_blank">+91- 9868303571

 

 


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--

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

 



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