[Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing
Selvaraj, Balamuruganand (B)
BSelvaraj at dow.com
Wed Jun 24 10:53:59 EDT 2009
GMOD-HelpDesk,
I like to modify the existing balloon hover for the reads seen in the
Alignment of the reads.
Although I am aware of the callback options, I wanted to know under
which module has the default hover has been included .
Secondly, I would like to know if there are any modules developed for
displaying the reads according to the quality scores.
Thanks.
Best regards,
Bala
________________________________
From: Lincoln Stein [mailto:lincoln.stein at gmail.com]
Sent: Tuesday, June 23, 2009 6:28 PM
To: Selvaraj, Balamuruganand (B)
Cc: help at gmod.org; balamuruganand at gmail.com;
gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
Sequencing
Hi,
Yes, the qscore() method had been returning the packed string of
binary qscore values. I realized this yesterday, and checked in a new
version of the module which returns the qscores as a regular array. The
method name is still qscore(). You can get the packed data using
_qscore().
Lincoln
On Tue, Jun 23, 2009 at 9:23 PM, Selvaraj, Balamuruganand (B)
<BSelvaraj at dow.com> wrote:
Hi GMOD-Users,
Is there a way by which I can get the quality scores of
the reads ?
I found qscore method in the AlignmentWrapper.pm which
is giving some other values which is hard to interpret.
So is there any other method which is already available
?
Best regards,
Bala
-----Original Message-----
From: Dave Clements, GMOD Help Desk
[mailto:gmodhelp at googlemail.com]
Sent: Monday, June 20, 2009 7:30 PM
To: Selvaraj, Balamuruganand (B)
Cc: gmod-gbrowse at lists.sourceforge.net;
balamuruganand at gmail.com
Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next
Generation Sequencing
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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------
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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>
>>
>>
>>
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>>
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>>
>
>
>
> --
> 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/
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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>
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