[Gmod-help] RE: [Gmod-gbrowse] NGS in GGB

Fri Mar 20 05:28:44 EDT 2009

Dave, 
I don't have anything to show right now as I have just started here. 
But I will be happy to send you some screen shots once I am up and running.
Which conference are you going to? Please send the talk if and when you can.

Thanks
Bernd

------------------------------------
Institute Pasteur
Bernd Jagla
Bioinformatician
bernd.jagla at pasteur.fr
Plate-form puces a ADN
Genopole / Institut Pasteur
28 rue du Docteur Roux
75724 Paris Cedex 15
France
tel: +33 (0) 140 61 35 13
------------------------------------

-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Tuesday, March 17, 2009 11:06 PM
To: Bernd Jagla
Cc: erant at psb.vib-ugent.be; gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] NGS in GGB

Erick, Bernd,

This came up in this week's GMOD teleconference, in a long thread on
the JBrowse list last week, and I'm giving a talk about using GMOD for
next generation sequencing data in a couple of weeks.  So, the
question is timely.  :-)  Lets see if we can keep the discussion
going:

I'd say that GMOD has ideas on this but I would hesitate to call them
plans at this point.  Read on.

I think this breaks into two broad areas:

1. Coping with the volume of data

If your users want to see each individual read then that can be a lot
of features in your database.  It's possible that we'll need to
develop some new techniques to make that tractable as datasets grow.
Lincoln suggested possibly using a distributed peer-to-peer model like
torrent.  This approach would presumably build on work in recent years
to extend GBrowse to support data sharing and user-uploadable tracks.

If your users don't care about individual tracks then the problem
becomes more tractable because you would only show summary/consensus
data in GBrowse.  Of course you still have to generate that
summary/consensus data, but that is outside of GBrowse.  I suspect
that over time, typical use cases will drift toward summary/consensus.
 (When reference assemblies were new, people also cared a lot about
the individual reads.)

2. Visualizing information that you couldn't gather without NGS.

Next generation sequencing allows us to ask a whole slew of new
questions, most of which, I'd bet, haven't even been thought of yet.
What can you discover when you have data from 1000 or 10,000
individuals?  Thinking a few years out, what can you do when you have
complete genomes from that many individuals?  I have no idea how to
deal with this because I have no idea what these questions will be.

For my part, I have a goal of documenting how to use GMOD for next
generation sequence data.  The PAG 2009 poster Erick referred to was a
start on that.  I'll also be giving a talk on this in two weeks.  By
mid-year I aim to have that poster and that talk translated into pages
on the GMOD wiki.

TO HELP ME WITH THAT (and with the presentation in two weeks), I HAVE
A REQUEST of anyone on this list who is using GBrowse to show NGS
data:  Can you send me (and/or this list) a link to your GBrowse
instance(s), preferably along with a short description of what NGS
data it is showing and how you show it.  I'd like to give people at
the workshop a feel for a wide range of possibilities, and it will
help me with the doc.

Thanks for reading this far, :-)

Dave C
GMOD Help Desk

Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

On Thu, Mar 12, 2009 at 7:52 AM, Bernd Jagla <bernd.jagla at pasteur.fr> wrote:
> I am currently setting up GBrowser GBrowser_karyotype to work with our
> NGS/Solexa data. As I am just working on this for a few days I am very
much
> open for discussions.
> Right now I am trying to understand the GFF3 format to convert the FASTQ
> files for later import into a MySQL database.
>
> Best,
>
> Bernd
>
>
>
> -----Original Message-----
> From: Erick Antezana [mailto:erant at psb.vib-ugent.be]
> Sent: Thursday, March 12, 2009 3:43 PM
> To: gmod-gbrowse at lists.sourceforge.net
> Subject: [Gmod-gbrowse] NGS in GGB
>
> Hi,
>
>  I have seen that teh GMOD team presented a poster at the last PAG meeting
> (http://gmod.org/w/images/6/6a/PAG2009NextGenSeqPoster.pdf). Also, I
> found that GBrowse is successfully exploited for visualisation (e.g.
> http://lalitponnala.googlepages.com/CHIposter.pdf)... I was wondering
> about the future development plans of GGB in that regard (to deal with
> NextGenSeq data)?
>
> thanks for the info,
> Erick
>
>
>
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