[Gmod-help] GMOD for Next Generation Sequencing

[Scott Cain]

Hi Bala,

I don't know anything about using eclipse for getting cvs checkouts,
but this page:

  http://lampsig.org/new/archives/17-LAMPSig-Class-2.0-Using-Eclipse-to-get-a-CVS-Project.html

has a description for how to do it as a developer, and one of the
commentors describes how to do it anonymously.

Does that help?

Scott


On Mon, Jun 1, 2009 at 10:41 AM, Selvaraj, Balamuruganand (B)
<BSelvaraj at dow.com> wrote:
>
> 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
>
>
>
> --
> Was this helpful?  Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
>
> 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
>
>



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