[hapmap.org #5047] Re: [Gmod-help] Re: NGS in GGB
Marcela K Tello-Ruiz via RT
help at hapmap.org
Fri May 22 14:35:35 EDT 2009
Hi Wei,
I am tempted to point Lincoln to our latest gbrowse directories, but I
would rather have you confirm that those are the latest working versions
of the glyphs.
Thanks,
Marcela
> [lstein at cshl.edu - Fri May 22 13:28:35 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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> > > >>>>
> > >
> >
> >
>
------------------------------------------------------------------------------
> > > >>>> Apps built with the Adobe(R) Flex(R) framework and Flex
> > > 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-
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> > > >>>> _______________________________________________
> > > >>>> Gmod-gbrowse mailing list
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> > > >>>> 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
> >
>
>
>
>
>
--
Marcela K. Tello-Ruiz
HapMap Data Coordination Center
Cold Spring Harbor Laboratory
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