[Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing
Selvaraj, Balamuruganand (B)
BSelvaraj at dow.com
Tue Jun 23 16:23:57 EDT 2009
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 15, 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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>>
>>
>>
>> --
>> 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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>>
>
>
>
> --
> 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
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
--
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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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