[Gmod-help] Re: NGS in GGB

Wed May 20 14:35:53 EDT 2009

Hi Dave,

Thanks for the link!  I hadn't seen this presentation posted, it has
good information, would you like me to forward your email to the list?

By the way, I sent a message to the list yesterday about an updated
ld_plot glyph I created, did you receive it?  What's the best way to
send code contributions?

yuri

On Wed, May 20, 2009 at 9:58 AM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> wrote:
> Hi Yuri,
>
> I did.  Some of it is in a talk I gave at an NGS meeting in April.  See
>  http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf
>
> However, I'm going to give updated versions of that talk in June using
> GBrowse 2.0 and the new SAMtools (SAM/BAM format) GBrowse adaptor.
> So, that talk will change quite a bit.  Once I'm back from the talks
> (mid-June), I'll convert the content to a web page.
>
> Dave C.
>
>
>
> 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
>
>
>
> On Tue, May 19, 2009 at 12:14 PM,  <ybendana at gmail.com> wrote:
>> Dave,
>>
>> Did you ever get any feedback regarding Gbrowse implementations for visualizing NGS data?
>>
>> thanks,
>>
>> yuri
>>
>> Dave Clements, GMOD Help Desk wrote:
>>>
>>> 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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>> Quoted from:  http://www.nabble.com/NGS-in-GGB-tp22477878p22568894.html
>>
>>
>