[Gmod-help] GMOD for Next Generation Sequencing

[Selvaraj, Balamuruganand (B)]

Dave,

Can you also let me know how we can connect to Gbrowse CVS. 
Although, I have all info (from Wiki)reg the CVS, I get error while I
try to add cvs host server as "gmod.cvs.sourceforge.net". 

Kindly let me know the following info.
Host:
Repository Path:

Kindly confirm, if the following information is correct
User:login
Password:\n

I am using windows platform and eclipse for getting the source code from
CVS.

Thanks in advance for your reply.

Best regards,
Bala

-----Original Message-----
From: Selvaraj, Balamuruganand (B) 
Sent: Monday, June 01, 2009 8:04 AM
To: 'help at gmod.org'
Subject: RE: [Gmod-help] GMOD for Next Generation Sequencing


Hi Dave,

Thanks for your reply.
Since, I am relatively new to Gbrowse, I am still figuring out many
things.

It will be really great if you could pass on some documentation
regarding the SAMtools adaptor.
I had another small question. Are there any utilities which convert the
sequence files from Solexa sequencing machines to SAM format.

Thanks again !

Best regards,
Bala 

-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Friday, May 29, 2009 5:16 PM
To: Selvaraj, Balamuruganand (B)
Cc: GMOD Help Desk
Subject: Re: [Gmod-help] GMOD for Next Generation Sequencing

Hi Bala,

Yes, although the presentation you are looking at did not use it
because it didn't yet exist.

In the last few months Lincoln has written a SAMtools database adaptor
for GBrowse.  It's available in CVS in GBrowse under the
gbrowse-adaptors directory.  I just got it really working on my laptop
today.

SAMtools is a set of programs that manipulate files in SAM and BAM
format.  BAM is the binary version of SAM.  SAM is an indexed,
compressed short read format.  The GBrowse adaptor reads from it.

However, some big caveats:
1. It is only useful in GBrowse 2.  In GBrowse 1 you can only specify
one adaptor.  Not so in 2.
2. It is not currently documented.

I'm giving two talks on this in the next two weeks.  The first talk
should be available on the GMOD web site around June 7.   A wiki
version of that talk should be available on the GMOD web site by the
end of June.

Is that soon enough?  If not I can go through my notes and try and
extract something meaningful.

Also note that the SAMtools adaptor only changes the E coli part of
that presentation.  Everything shown in the threespine stickleback is
still done using long existing technology (and lots of disk space).

Dave C.

On Fri, May 29, 2009 at 1:58 PM, Selvaraj, Balamuruganand (B)
<BSelvaraj at dow.com> wrote:
>
> Hi Dave Clement,
>
> I am currently trying to use Gbrowse for view Next generation
Sequencing
> alignments.
> I just saw slides of the GMOD's NGS workshop in Germany
> (http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf)
>
> I wanted to know if the plugins for GMOD have already been developed.
>
> Thanks for your reply.
>
> Best regards,
> Bala



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Learn more about GMOD at:
  SMBE:
http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
  Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
  AGA Next Gen Seq in Non-Models:
http://www.regonline.com/Nextgeneration