Hi,<br><br>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().<br>
<br>Lincoln<br><br><div class="gmail_quote">On Tue, Jun 23, 2009 at 9:23 PM, Selvaraj, Balamuruganand (B) <span dir="ltr"><<a href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Hi GMOD-Users,<br>
<br>
Is there a way by which I can get the quality scores of the reads ?<br>
I found qscore method in the AlignmentWrapper.pm which is giving some other values which is hard to interpret.<br>
<br>
So is there any other method which is already available ?<br>
<br>
Best regards,<br>
<div class="im">Bala<br>
<br>
-----Original Message-----<br>
From: Dave Clements, GMOD Help Desk [mailto:<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>]<br>
</div><div class="im">Sent: Monday, June 15, 2009 7:30 PM<br>
To: Selvaraj, Balamuruganand (B)<br>
</div><div><div></div><div class="h5">Cc: <a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a>; <a href="mailto:balamuruganand@gmail.com">balamuruganand@gmail.com</a><br>
Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing<br>
<br>
Hi Bala,<br>
<br>
You do need to add track definitions. From the E. coli example shown<br>
in the SMBE talk (which is now available at:<br>
<a href="http://gmod.org/wiki/Image:GMODGBrowseSMBE2009.pdf" target="_blank">http://gmod.org/wiki/Image:GMODGBrowseSMBE2009.pdf</a>), here are 3 track<br>
examples:<br>
<br>
Note that with the versions of the software I was using (see previous<br>
response) I could not get semantic zooming to work with these tracks.<br>
(Not sure if that was me or the software though.) Meaning, if you<br>
zoom out to 100Kbp, your request will never come back.<br>
<br>
Hope this helps,<br>
<br>
Dave C<br>
<br>
[TRACK DEFAULTS]<br>
glyph = generic<br>
height = 10<br>
bgcolor = lightgrey<br>
fgcolor = black<br>
font2color = blue<br>
label density = 25<br>
bump density = 100<br>
hbumppad = 6<br>
min_score = 0<br>
max_score = 200<br>
# where to link to when user clicks in detailed view<br>
link = AUTO<br>
<br>
#<br>
# DERIVED 1<br>
#<br>
<br>
[Derived1Reads]<br>
feature = match<br>
glyph = segments<br>
draw_target = 1<br>
show_mismatch = 1<br>
mismatch_color = red<br>
database = ecolisam<br>
bgcolor = blue<br>
fgcolor = white<br>
height = 5<br>
label = sub {shift->display_name}<br>
label density = 50<br>
bump = fast<br>
key = Derived1 reads<br>
category = Reads<br>
<br>
[Derived1CoverageXyplot]<br>
feature = coverage:2000<br>
glyph = wiggle_xyplot<br>
database = ecolisam<br>
height = 50<br>
fgcolor = black<br>
bicolor_pivot = 20<br>
pos_color = blue<br>
neg_color = red<br>
key = Derived1 coverage (xyplot)<br>
category = Reads<br>
label = 0 # Labels on wiggle tracks are redundant.<br>
<br>
[Derived1CoverageDensity]<br>
feature = coverage:2000<br>
glyph = wiggle_density<br>
database = ecolisam<br>
height = 30<br>
bgcolor = blue<br>
bicolor_pivot = 20<br>
pos_color = blue<br>
neg_color = red<br>
key = Derived1 coverage (density plot)<br>
category = Reads<br>
label = 0 # labels on wiggle tracks are redundant<br>
<br>
<br>
On Fri, Jun 12, 2009 at 2:07 PM, Selvaraj, Balamuruganand<br>
(B)<<a href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</a>> wrote:<br>
> Dave, Lincoln,<br>
><br>
> I am able to see the seq1 (fasta and Sam files obtained from the example<br>
> provided in SAMTools) in the overview section.<br>
> However, I am not able to see the alignments. Do we need to add some tracks<br>
> in the conf file to see them ?<br>
><br>
> Thanks for your reply.<br>
><br>
> Best regards,<br>
> Bala<br>
><br>
> ________________________________<br>
> From: Selvaraj, Balamuruganand (B) [mailto:<a href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</a>]<br>
> Sent: Friday, June 12, 2009 8:30 AM<br>
> To: <a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a><br>
> Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing<br>
><br>
> Dave,<br>
><br>
> I am able to get it in the pull down menu. However, on choosing it - I don't<br>
> see any alignments for NGS.<br>
> Attached screenshot of what I am getting.<br>
><br>
> The footer of gbrowse points towards 1.988. Is that an issue ?<br>
><br>
> Thanks,<br>
> -Bala<br>
><br>
> ________________________________<br>
> From: Dave Clements, GMOD Help Desk [mailto:<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>]<br>
> Sent: Thursday, June 11, 2009 6:48 PM<br>
> To: Selvaraj, Balamuruganand (B)<br>
> Cc: <a href="mailto:lstein@cshl.edu">lstein@cshl.edu</a>; <a href="mailto:balamuruganand@gmail.com">balamuruganand@gmail.com</a>;<br>
> <a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a><br>
> Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing<br>
><br>
> Hi Bala,<br>
> Is there a "Data Source" pull down menu on your Yeast page? It should list<br>
> the name of your other source, as defined in your new conf file. If it does<br>
> not list it, then I believe that it means GBrowse 2 was unable to process<br>
> that new conf file. Check your apache error log for any problems. Also,<br>
> look at the permissions on your conf file and on your bam files and<br>
> directories. They should be the same as those in the yeast example.<br>
> Ciao,<br>
> Dave C<br>
> On Thu, Jun 11, 2009 at 6:02 PM, Selvaraj, Balamuruganand (B)<br>
> <<a href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</a>> wrote:<br>
>><br>
>> Lincoln,<br>
>><br>
>> I have created a new BAMTest folder inside /var/html/gbrowse2/databases/<br>
>> and also added added a new conf file under /etc/gbrowse2.<br>
>> But still I am being directed to Yeast page. Do I need to something else.<br>
>> Let me know.<br>
>><br>
>> -Bala<br>
>><br>
>> ________________________________<br>
>> From: <a href="mailto:lincoln.stein@gmail.com">lincoln.stein@gmail.com</a> [mailto:<a href="mailto:lincoln.stein@gmail.com">lincoln.stein@gmail.com</a>] On Behalf<br>
>> Of Lincoln Stein<br>
>> Sent: Friday, June 05, 2009 2:30 PM<br>
>> To: Selvaraj, Balamuruganand (B)<br>
>> Cc: <a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a><br>
>> Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation<br>
>> Sequencing<br>
>><br>
>> It only works with BAM format files. That is, it is an adaptor for BAM<br>
>> files that makes the BAM file act like a database.<br>
>><br>
>> Here is the configuration section:<br>
>><br>
>><br>
>> db_adaptor = Bio::DB::Sam<br>
>> db_args = -fasta /var/www/gbrowse2/databases/bamtest/ex1.fa<br>
>> -bam /var/www/gbrowse2/databases/bamtest/ex1.bam<br>
>><br>
>><br>
>> The BAM and FA files need to be created and indexed before you try this.<br>
>><br>
>> Lincoln<br>
>><br>
>><br>
>> On Fri, Jun 5, 2009 at 2:09 PM, Selvaraj, Balamuruganand (B)<br>
>> <<a href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</a>> wrote:<br>
>>><br>
>>> Dave / GMOD help Desk,<br>
>>><br>
>>> I had few question reg the Next generation Sequencing.<br>
>>> Does the SAMTools adaptor designed for the Next generation Sequencing<br>
>>> works with "in memory database"<br>
>>> or it works only with external database.<br>
>>><br>
>>> Can you provide us with some details of configuring the adaptor if you<br>
>>> have any notes on it?<br>
>>><br>
>>> -Bala<br>
>>><br>
>>><br>
>>> -----Original Message-----<br>
>>> From: Dave Clements, GMOD Help Desk [mailto:<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>]<br>
>>> Sent: Friday, May 29, 2009 5:16 PM<br>
>>> To: Selvaraj, Balamuruganand (B)<br>
>>> Cc: GMOD Help Desk<br>
>>> Subject: Re: [Gmod-help] GMOD for Next Generation Sequencing<br>
>>><br>
>>> Hi Bala,<br>
>>><br>
>>> Yes, although the presentation you are looking at did not use it<br>
>>> because it didn't yet exist.<br>
>>><br>
>>> In the last few months Lincoln has written a SAMtools database adaptor<br>
>>> for GBrowse. It's available in CVS in GBrowse under the<br>
>>> gbrowse-adaptors directory. I just got it really working on my laptop<br>
>>> today.<br>
>>><br>
>>> SAMtools is a set of programs that manipulate files in SAM and BAM<br>
>>> format. BAM is the binary version of SAM. SAM is an indexed,<br>
>>> compressed short read format. The GBrowse adaptor reads from it.<br>
>>><br>
>>> However, some big caveats:<br>
>>> 1. It is only useful in GBrowse 2. In GBrowse 1 you can only specify<br>
>>> one adaptor. Not so in 2.<br>
>>> 2. It is not currently documented.<br>
>>><br>
>>> I'm giving two talks on this in the next two weeks. The first talk<br>
>>> should be available on the GMOD web site around June 7. A wiki<br>
>>> version of that talk should be available on the GMOD web site by the<br>
>>> end of June.<br>
>>><br>
>>> Is that soon enough? If not I can go through my notes and try and<br>
>>> extract something meaningful.<br>
>>><br>
>>> Also note that the SAMtools adaptor only changes the E coli part of<br>
>>> that presentation. Everything shown in the threespine stickleback is<br>
>>> still done using long existing technology (and lots of disk space).<br>
>>><br>
>>> Dave C.<br>
>>><br>
>>> On Fri, May 29, 2009 at 1:58 PM, Selvaraj, Balamuruganand (B)<br>
>>> <<a href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</a>> wrote:<br>
>>> ><br>
>>> > Hi Dave Clement,<br>
>>> ><br>
>>> > I am currently trying to use Gbrowse for view Next generation<br>
>>> Sequencing<br>
>>> > alignments.<br>
>>> > I just saw slides of the GMOD's NGS workshop in Germany<br>
>>> > (<a href="http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf" target="_blank">http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf</a>)<br>
>>> ><br>
>>> > I wanted to know if the plugins for GMOD have already been developed.<br>
>>> ><br>
>>> > Thanks for your reply.<br>
>>> ><br>
>>> > Best regards,<br>
>>> > Bala<br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>> Was this helpful? Let us know at<br>
>>> <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
>>><br>
>>> Learn more about GMOD at:<br>
>>> SMBE:<br>
>>> <a href="http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27" target="_blank">http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27</a><br>
>>> Arthropod Genomics: <a href="http://www.k-state.edu/agc/symp2009/seminar.html" target="_blank">http://www.k-state.edu/agc/symp2009/seminar.html</a><br>
>>> AGA Next Gen Seq in Non-Models:<br>
>>> <a href="http://www.regonline.com/Nextgeneration" target="_blank">http://www.regonline.com/Nextgeneration</a><br>
>>><br>
>>><br>
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>><br>
>><br>
>><br>
>> --<br>
>> Lincoln D. Stein<br>
>> Director, Informatics and Biocomputing Platform<br>
>> Ontario Institute for Cancer Research<br>
>> 101 College St., Suite 800<br>
>> Toronto, ON, Canada M5G0A3<br>
>> 416 673-8514<br>
>> Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>
>><br>
>><br>
>> ------------------------------------------------------------------------------<br>
>> Crystal Reports - New Free Runtime and 30 Day Trial<br>
>> Check out the new simplified licensing option that enables unlimited<br>
>> royalty-free distribution of the report engine for externally facing<br>
>> server and web deployment.<br>
>> <a href="http://p.sf.net/sfu/businessobjects" target="_blank">http://p.sf.net/sfu/businessobjects</a><br>
>> _______________________________________________<br>
>> Gmod-gbrowse mailing list<br>
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>><br>
><br>
><br>
><br>
> --<br>
> Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
><br>
> Learn more about GMOD at:<br>
> AGA Next Gen Seq in Non-Models: <a href="http://www.regonline.com/Nextgeneration" target="_blank">http://www.regonline.com/Nextgeneration</a><br>
> Galaxy Workshop at NBIC: <a href="http://www.nbic.nl/nbic/newsevents/Galaxy/" target="_blank">http://www.nbic.nl/nbic/newsevents/Galaxy/</a><br>
><br>
> ------------------------------------------------------------------------------<br>
> Crystal Reports - New Free Runtime and 30 Day Trial<br>
> Check out the new simplified licensing option that enables unlimited<br>
> royalty-free distribution of the report engine for externally facing<br>
> server and web deployment.<br>
> <a href="http://p.sf.net/sfu/businessobjects" target="_blank">http://p.sf.net/sfu/businessobjects</a><br>
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><br>
><br>
<br>
<br>
<br>
--<br>
Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
<br>
Learn more about GMOD at:<br>
AGA Next Gen Seq in Non-Models: <a href="http://www.regonline.com/Nextgeneration" target="_blank">http://www.regonline.com/Nextgeneration</a><br>
Galaxy Workshop at NBIC: <a href="http://www.nbic.nl/nbic/newsevents/Galaxy/" target="_blank">http://www.nbic.nl/nbic/newsevents/Galaxy/</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>