[Gmod-help] Re: NGS in GGB

Thu May 21 16:54:28 EDT 2009

Hi Yuri, (and Marcela, Lincoln, and Scott)

I wouldn't send out the link to the talk just yet.  The technology for
displaying NGS data in GBrowse has greatly improved in the last month
or so, and I'll post a new talk (or two) in mid-June.

I'm not sure what the best way to get ld_plot into the Bio::Graphics
CVS repository is.  I think ld_plot is currently controlled by the
HapMap project.

Marcela, would HapMap be willing to contribute ld_plot to Bio::Graphics?

Yuri, if HapMap agrees to contribute, then you will need to convince
Lincoln and/or Scott that your updates should also go in.

Thanks,

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

2009/5/20 Yuri Titov Bendaña <ybendana at gmail.com>:
> 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
>>>
>>>
>>
>