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<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>GMOD-HelpDesk,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>I like to modify the existing balloon hover for the reads
seen in the Alignment of the reads. </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>Although I am aware of the callback options, I wanted to
know under which module has the default hover has been included
.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>Secondly, I would like to know if there are any modules
developed for displaying the reads according to the quality
scores.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009></SPAN><SPAN
class=146404714-24062009><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>Thanks.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>Best regards,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=146404714-24062009><FONT face=Arial
color=#0000ff size=2>Bala</FONT></SPAN><BR></DIV>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> Lincoln Stein
[mailto:lincoln.stein@gmail.com] <BR><B>Sent:</B> Tuesday, June 23, 2009 6:28
PM<BR><B>To:</B> Selvaraj, Balamuruganand (B)<BR><B>Cc:</B> help@gmod.org;
balamuruganand@gmail.com;
gmod-gbrowse@lists.sourceforge.net<BR><B>Subject:</B> Re: [Gmod-gbrowse]
[Gmod-help] GMOD for Next Generation Sequencing<BR></FONT><BR></DIV>
<DIV></DIV>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="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><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 <SPAN
class=922441213-24062009>20</SPAN>, 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>>>>
------------------------------------------------------------------------------<BR>>>>
OpenSolaris 2009.06 is a cutting edge operating system for
enterprises<BR>>>> looking to deploy the next generation of Solaris
that includes the latest<BR>>>> innovations from Sun and the
OpenSource community. Download a copy and<BR>>>> enjoy capabilities
such as Networking, Storage and Virtualization.<BR>>>> Go to: <A
href="http://p.sf.net/sfu/opensolaris-get"
target=_blank>http://p.sf.net/sfu/opensolaris-get</A><BR>>>>
_______________________________________________<BR>>>> Gmod-gbrowse
mailing list<BR>>>> <A
href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</A><BR>>>>
<A href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse"
target=_blank>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</A><BR>>><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>>> <A
href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</A><BR>>>
<A href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse"
target=_blank>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</A><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>><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>> <A
href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</A><BR>>
<A href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse"
target=_blank>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</A><BR>><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><BR>------------------------------------------------------------------------------<BR>_______________________________________________<BR>Gmod-gbrowse
mailing list<BR><A
href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</A><BR><A
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target=_blank>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</A><BR></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></BLOCKQUOTE></BODY></HTML>