[Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing
Balamuruganand Selvaraj
balamuruganand at gmail.com
Tue Jun 23 21:59:01 EDT 2009
Hi Lincoln,
I don't see any documentation for using the modules in the latest
Bio-samtools.
If possible can you send the file to me.
Also, have you moved the qscore method from AlignWrapper to Alignment.pm ?
Thanks.
Best regards,
Bala
On Wed, Jun 24, 2009 at 3:59 AM, Lincoln Stein <lstein at cshl.edu> wrote:
> 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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>> >>
>> >>
>> >>
>> >> --
>> >> 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
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>> >> _______________________________________________
>> >> 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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