help regardng Gbrowse_syn .conf file

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

help regardng Gbrowse_syn .conf file

Meenu
Dear Sir

I have started Synteny analysis only for 1 chromosome (because full genome need more space and memory)  as i know that bos chromosome 29 have synteny relationship  with human chr 11, so i have done complete alignment for bos and human chromosome.

After that I prepare .conf file , but when i am running on browser its showing both species but after clicking on coordinates its showing coordinates not found in database.

I think there is some problem in mentioning coordinates in .synconf file (i have mention the coordinated as given in map file).

Please let me know how to mention correct coordinates .

I am attaching the screen shot, .map file and .synconf file.

Any suggestion will be appreciable.

Thanks

--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

humansyn.synconf (1K) Download Attachment
map (2K) Download Attachment
Screenshot-1.png (442K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: help regardng Gbrowse_syn .conf file

Sheldon McKay
Hi Meenu,

The coordinates shown in the .synconf file are just examples that are shown on the browser page.  If your query is showing coordinates that are not found in your database, it means that the mapped alignments are in regions not loaded in you species' databases or that your reference sequences are not correctly loaded in your species' databases.  These kind of data are never encoded in configuration files, as Scott Cain pointed out in a previous post to you.  If you are using only a portion of one genome, you must filter out-of-range alignments prior to loading the alignment database.  This filtering must remove alignments that map to regions outside of the reference sequences in your species' database for *all* species in the alignment.  I do not recommend doing this, however, as I discussed in a previous post to you.

If your space and memory are really that limited, I would recommend using a cloud based Amazon EC2 server at a modest cost (http://gmod.org/wiki/Cloud) or using free cloud computing via iPlant (https://atmo.iplantcollaborative.org).  For the latter, you can use the Ubuntu image (easy installation of GBrowse, which includes GBrowse_syn, for Ubuntu is described at http://gmod.org/wiki/GBrowse_Ubuntu_HOWTO).

Sheldon


Sheldon McKay, PhD
Computational Biologist
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Rd
Cold Spring Harbor, NY 11724
(516) 367-5185
www.dnalc.org


On Fri, Feb 1, 2013 at 4:59 AM, Meenu Chopra <[hidden email]> wrote:
Dear Sir

I have started Synteny analysis only for 1 chromosome (because full genome need more space and memory)  as i know that bos chromosome 29 have synteny relationship  with human chr 11, so i have done complete alignment for bos and human chromosome.

After that I prepare .conf file , but when i am running on browser its showing both species but after clicking on coordinates its showing coordinates not found in database.

I think there is some problem in mentioning coordinates in .synconf file (i have mention the coordinated as given in map file).

Please let me know how to mention correct coordinates .

I am attaching the screen shot, .map file and .synconf file.

Any suggestion will be appreciable.

Thanks

--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse