[Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing
Lincoln Stein
lstein at cshl.edu
Tue Jun 23 18:29:20 EDT 2009
Hi,
In the most recently checked in version of Bio-SamTools there is
documentation about using the module underneath GBrowse2.
You always seem to be just one day ahead of me!!!!
Lincoln
On Tue, Jun 16, 2009 at 12:30 AM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:
> Hi Bala,
>
> You do need to add track definitions. From the E. coli example shown
> in the SMBE talk (which is now available at:
> http://gmod.org/wiki/Image:GMODGBrowseSMBE2009.pdf), here are 3 track
> examples:
>
> Note that with the versions of the software I was using (see previous
> response) I could not get semantic zooming to work with these tracks.
> (Not sure if that was me or the software though.) Meaning, if you
> zoom out to 100Kbp, your request will never come back.
>
> Hope this helps,
>
> Dave C
>
> [TRACK DEFAULTS]
> glyph = generic
> height = 10
> bgcolor = lightgrey
> fgcolor = black
> font2color = blue
> label density = 25
> bump density = 100
> hbumppad = 6
> min_score = 0
> max_score = 200
> # where to link to when user clicks in detailed view
> link = AUTO
>
> #
> # DERIVED 1
> #
>
> [Derived1Reads]
> feature = match
> glyph = segments
> draw_target = 1
> show_mismatch = 1
> mismatch_color = red
> database = ecolisam
> bgcolor = blue
> fgcolor = white
> height = 5
> label = sub {shift->display_name}
> label density = 50
> bump = fast
> key = Derived1 reads
> category = Reads
>
> [Derived1CoverageXyplot]
> feature = coverage:2000
> glyph = wiggle_xyplot
> database = ecolisam
> height = 50
> fgcolor = black
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key = Derived1 coverage (xyplot)
> category = Reads
> label = 0 # Labels on wiggle tracks are redundant.
>
> [Derived1CoverageDensity]
> feature = coverage:2000
> glyph = wiggle_density
> database = ecolisam
> height = 30
> bgcolor = blue
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key = Derived1 coverage (density plot)
> category = Reads
> label = 0 # labels on wiggle tracks are redundant
>
>
> On Fri, Jun 12, 2009 at 2:07 PM, Selvaraj, Balamuruganand
> (B)<BSelvaraj at dow.com> wrote:
> > Dave, Lincoln,
> >
> > I am able to see the seq1 (fasta and Sam files obtained from the example
> > provided in SAMTools) in the overview section.
> > However, I am not able to see the alignments. Do we need to add some
> tracks
> > in the conf file to see them ?
> >
> > Thanks for your reply.
> >
> > Best regards,
> > Bala
> >
> > ________________________________
> > From: Selvaraj, Balamuruganand (B) [mailto:BSelvaraj at dow.com]
> > Sent: Friday, June 12, 2009 8:30 AM
> > To: gmod-gbrowse at lists.sourceforge.net
> > Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
> Sequencing
> >
> > Dave,
> >
> > I am able to get it in the pull down menu. However, on choosing it - I
> don't
> > see any alignments for NGS.
> > Attached screenshot of what I am getting.
> >
> > The footer of gbrowse points towards 1.988. Is that an issue ?
> >
> > Thanks,
> > -Bala
> >
> > ________________________________
> > From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com]
> > Sent: Thursday, June 11, 2009 6:48 PM
> > To: Selvaraj, Balamuruganand (B)
> > Cc: lstein at cshl.edu; balamuruganand at gmail.com;
> > gmod-gbrowse at lists.sourceforge.net
> > Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
> Sequencing
> >
> > Hi Bala,
> > Is there a "Data Source" pull down menu on your Yeast page? It should
> list
> > the name of your other source, as defined in your new conf file. If it
> does
> > not list it, then I believe that it means GBrowse 2 was unable to process
> > that new conf file. Check your apache error log for any problems. Also,
> > look at the permissions on your conf file and on your bam files and
> > directories. They should be the same as those in the yeast example.
> > Ciao,
> > Dave C
> > On Thu, Jun 11, 2009 at 6:02 PM, Selvaraj, Balamuruganand (B)
> > <BSelvaraj at dow.com> wrote:
> >>
> >> Lincoln,
> >>
> >> I have created a new BAMTest folder inside /var/html/gbrowse2/databases/
> >> and also added added a new conf file under /etc/gbrowse2.
> >> But still I am being directed to Yeast page. Do I need to something
> else.
> >> Let me know.
> >>
> >> -Bala
> >>
> >> ________________________________
> >> From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com] On
> Behalf
> >> Of Lincoln Stein
> >> Sent: Friday, June 05, 2009 2:30 PM
> >> To: Selvaraj, Balamuruganand (B)
> >> Cc: gmod-gbrowse at lists.sourceforge.net
> >> Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
> >> Sequencing
> >>
> >> It only works with BAM format files. That is, it is an adaptor for BAM
> >> files that makes the BAM file act like a database.
> >>
> >> Here is the configuration section:
> >>
> >>
> >> db_adaptor = Bio::DB::Sam
> >> db_args = -fasta /var/www/gbrowse2/databases/bamtest/ex1.fa
> >> -bam /var/www/gbrowse2/databases/bamtest/ex1.bam
> >>
> >>
> >> The BAM and FA files need to be created and indexed before you try this.
> >>
> >> Lincoln
> >>
> >>
> >> On Fri, Jun 5, 2009 at 2:09 PM, Selvaraj, Balamuruganand (B)
> >> <BSelvaraj at dow.com> wrote:
> >>>
> >>> Dave / GMOD help Desk,
> >>>
> >>> I had few question reg the Next generation Sequencing.
> >>> Does the SAMTools adaptor designed for the Next generation Sequencing
> >>> works with "in memory database"
> >>> or it works only with external database.
> >>>
> >>> Can you provide us with some details of configuring the adaptor if you
> >>> have any notes on it?
> >>>
> >>> -Bala
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com]
> >>> Sent: Friday, May 29, 2009 5:16 PM
> >>> To: Selvaraj, Balamuruganand (B)
> >>> Cc: GMOD Help Desk
> >>> Subject: Re: [Gmod-help] GMOD for Next Generation Sequencing
> >>>
> >>> Hi Bala,
> >>>
> >>> Yes, although the presentation you are looking at did not use it
> >>> because it didn't yet exist.
> >>>
> >>> In the last few months Lincoln has written a SAMtools database adaptor
> >>> for GBrowse. It's available in CVS in GBrowse under the
> >>> gbrowse-adaptors directory. I just got it really working on my laptop
> >>> today.
> >>>
> >>> SAMtools is a set of programs that manipulate files in SAM and BAM
> >>> format. BAM is the binary version of SAM. SAM is an indexed,
> >>> compressed short read format. The GBrowse adaptor reads from it.
> >>>
> >>> However, some big caveats:
> >>> 1. It is only useful in GBrowse 2. In GBrowse 1 you can only specify
> >>> one adaptor. Not so in 2.
> >>> 2. It is not currently documented.
> >>>
> >>> I'm giving two talks on this in the next two weeks. The first talk
> >>> should be available on the GMOD web site around June 7. A wiki
> >>> version of that talk should be available on the GMOD web site by the
> >>> end of June.
> >>>
> >>> Is that soon enough? If not I can go through my notes and try and
> >>> extract something meaningful.
> >>>
> >>> Also note that the SAMtools adaptor only changes the E coli part of
> >>> that presentation. Everything shown in the threespine stickleback is
> >>> still done using long existing technology (and lots of disk space).
> >>>
> >>> Dave C.
> >>>
> >>> On Fri, May 29, 2009 at 1:58 PM, Selvaraj, Balamuruganand (B)
> >>> <BSelvaraj at dow.com> wrote:
> >>> >
> >>> > Hi Dave Clement,
> >>> >
> >>> > I am currently trying to use Gbrowse for view Next generation
> >>> Sequencing
> >>> > alignments.
> >>> > I just saw slides of the GMOD's NGS workshop in Germany
> >>> > (http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf)
> >>> >
> >>> > I wanted to know if the plugins for GMOD have already been developed.
> >>> >
> >>> > Thanks for your reply.
> >>> >
> >>> > Best regards,
> >>> > Bala
> >>>
> >>>
> >>>
> >>> --
> >>> 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
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
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> latest
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> >>> _______________________________________________
> >>> Gmod-gbrowse mailing list
> >>> Gmod-gbrowse at lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >>
> >>
> >>
> >> --
> >> 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>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Crystal Reports - New Free Runtime and 30 Day Trial
> >> Check out the new simplified licensing option that enables unlimited
> >> royalty-free distribution of the report engine for externally facing
> >> server and web deployment.
> >> http://p.sf.net/sfu/businessobjects
> >> _______________________________________________
> >> Gmod-gbrowse mailing list
> >> Gmod-gbrowse at lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >>
> >
> >
> >
> > --
> > Was this helpful? Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
> >
> > Learn more about GMOD at:
> > AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration
> > Galaxy Workshop at NBIC: http://www.nbic.nl/nbic/newsevents/Galaxy/
> >
> >
> ------------------------------------------------------------------------------
> > Crystal Reports - New Free Runtime and 30 Day Trial
> > Check out the new simplified licensing option that enables unlimited
> > royalty-free distribution of the report engine for externally facing
> > server and web deployment.
> > http://p.sf.net/sfu/businessobjects
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> >
>
>
>
> --
> Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at:
> AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration
> Galaxy Workshop at NBIC: http://www.nbic.nl/nbic/newsevents/Galaxy/
>
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
--
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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