[Gmod-help] GMOD for Next Generation Sequencing

[Selvaraj, Balamuruganand (B)]

Dave,

I am facing issues with SAMTools and Bio::DB::Sam modules. Since you
said that you had the NGS analysis working on your laptop, I thought I
will ask you for your help.

When I am trying to compile the Bio::DB::SAM module, I get an error
asking me to compile with -fPIC.
In spite of doing compilation with -fPIC, I again get error messages.

Is there a way out of this error. It will be great if you could pass on
some notes or last week presentation if it contains details about the
installation.

Thanks.

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