[hapmap.org #5047] Re: [Gmod-help] Re: NGS in GGB

Fri May 22 13:27:00 EDT 2009

Hi Marcela,

I'm happy to enter the glyphs into Bio::Graphics.  I just need to know which
ones to enter; I understand there have been many revisions recently and I am
confused about which ones work.

Lincoln

On Fri, May 22, 2009 at 12:13 PM, Marcela K Tello-Ruiz via RT <
help at hapmap.org> wrote:

> Hi Dave et al,
>
> All the code we developed for use hapmap.org is freely available and for
> public distribution, looks like we lagged behind in contributing the LD
> plot related glyphs to Bio::Graphics and would be happy to catch up.
>
> There is one thing I need to clarify. The current version of the LD plot
> plugin is using a new glyph, called the myreverseplot.pm, which was
> originally created by Lincoln. None of our plugins is using ld_plot.pm
> right now, whose author was also Lincoln.
>
> Lincoln - Would you be willing to enter the LD plot glyphs into
> Bio::Graphics or should we go ahead and do it on your behalf?
>
> Thanks,
>
> Marcela
>
>
>
> > [help at gmod.org - Thu May 21 16:55:30 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).<http://lalitponnala.googlepages.com/CHIposter.pdf%29.>..
> 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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> > >>>>>
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> >
>
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> > >>>>>
> > >>>>
> > >>>>
> >
>
> ------------------------------------------------------------------------------
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> > Builder(TM) are
> > >>>> powering Web 2.0 with engaging, cross-platform capabilities.
> > Quickly and
> > >>>> easily build your RIAs with Flex Builder, the Eclipse(TM)based
> > development
> > >>>> software that enables intelligent coding and step-through
> > debugging.
> > >>>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> > >>>> _______________________________________________
> > >>>> Gmod-gbrowse mailing list
> > >>>> Gmod-gbrowse at lists.sourceforge.net
> > >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >>>>
> > >>>>
> > >>> Quoted from:  http://www.nabble.com/NGS-in-GGB-
> > tp22477878p22568894.html
> > >>>
> > >>>
> > >>
> > >
> >
> >
> >
> --
> Marcela K. Tello-Ruiz
> HapMap Data Coordination Center
> Cold Spring Harbor Laboratory
>

-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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