Bio-SamTools and Gbrowse1.7
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Bio-SamTools and Gbrowse1.7
by Wes Barris
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Hi,
This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) suggests that Gbrowse 1.7 can be used to display coverage density and XY plots from .bam (SamTools) files. I am familiar with samtools. I have .bam files and have created a gbrowse .conf file using the Bio::DB::Sam adaptor. I can successfully display the individual reads using a stanza that includes: feature = match glyph = segments My question is: "How can I display coverage density and XY plots from the .bam file?" I found the following stanza in a previous post but I don't have an explanation of the "feature" or "database" lines: [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) label = 0 # Labels on wiggle tracks are redundant. Can someone provide me with a sample stanza for gbrowse 1.7? -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Bio-SamTools and Gbrowse1.7
by Scott Cain-4
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Hi Wes,
Attached are the two conf files that I used to create the poster for GBrowse 1.70 (I think I really used 1.71b from svn, but that shouldn't matter, but you do need to get Bio-DB-Sam from svn). Let me know if you have any questions. Scott On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> wrote: > Hi, > > This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) > suggests that Gbrowse 1.7 can be used to display coverage density > and XY plots from .bam (SamTools) files. > > I am familiar with samtools. I have .bam files and have created > a gbrowse .conf file using the Bio::DB::Sam adaptor. I can successfully > display the individual reads using a stanza that includes: > > feature = match > glyph = segments > > My question is: "How can I display coverage density and XY plots > from the .bam file?" I found the following stanza in a previous > post but I don't have an explanation of the "feature" or "database" > lines: > > [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) > label = 0 # Labels on wiggle tracks are redundant. > > Can someone provide me with a sample stanza for gbrowse 1.7? > -- > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Bio-SamTools and Gbrowse1.7
by Wes Barris
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Scott Cain wrote:
> Hi Wes, > > Attached are the two conf files that I used to create the poster for > GBrowse 1.70 (I think I really used 1.71b from svn, but that shouldn't > matter, but you do need to get Bio-DB-Sam from svn). Let me know if > you have any questions. Hi Scott, I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without the curses or zlib libraries because I am not trying to use it to create .bam files or to use the samtools tview option). I just did an svn checkout of Bio-Samtools and built and installed that. Here are portions of my .conf file: [GENERAL] description = MrsFast db_adaptor = Bio::DB::Sam db_args = -bam /work/bs/tmp/hmgu_080725_HWI-EAS186_307FYAAXX_1.sorted.bam [Match] feature = match glyph = segments bgcolor = blue fgcolor = blue height = 3 label = sub {shift->display_name} label density = 50 bump = fast key = BAM Alignments [CoverageXyplot] feature = coverage:10000 glyph = wiggle_xyplot height = 50 fgcolor = black bicolor_pivot = 20 pos_color = blue neg_color = red key = XY plot label = 0 # Labels on wiggle tracks are redundant. The "Match" stanza works. I can see the individual reads displayed in GBrowse. However, the coverage plot shows an empty xy plot in GBrowse. There are no errors in my apache error log file. What else could I be missing? > Scott > > > On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> wrote: >> Hi, >> >> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) >> suggests that Gbrowse 1.7 can be used to display coverage density >> and XY plots from .bam (SamTools) files. >> >> I am familiar with samtools. I have .bam files and have created >> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can successfully >> display the individual reads using a stanza that includes: >> >> feature = match >> glyph = segments >> >> My question is: "How can I display coverage density and XY plots >> from the .bam file?" I found the following stanza in a previous >> post but I don't have an explanation of the "feature" or "database" >> lines: >> >> [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) >> label = 0 # Labels on wiggle tracks are redundant. >> >> Can someone provide me with a sample stanza for gbrowse 1.7? >> -- >> Wes Barris <wes.barris@...> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [ExternalEmail] Re: Bio-SamTools and Gbrowse1.7
by Wes Barris
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I'm not sure why but I don't seem to be getting any responses to my
question about getting Bio-Samtools to work so I'll try again... I am running Gbrowse 1.71b, Bio-Samtools from svn, samtools-0.1.6, and Bio-Graphics 1.982. I have a .bam file from which I would like to view alignments, coverage density and a coverage XY plot. Gbrowse displays the alignment but does not display either the density or XY plot. I am assuming that since the alignments are being displayed that the data is being read properly from the .bam file. I can't figure out why the wiggle tracks do not display any data. Here are my track definitions (the first of which works): [Match] feature = match glyph = segments bgcolor = blue fgcolor = blue height = 3 label = sub {shift->display_name} label density = 50 bump = fast key = BAM Alignments [CoverageXyplot] feature = coverage:10000 glyph = wiggle_xyplot height = 50 fgcolor = black bicolor_pivot = 20 pos_color = blue neg_color = red key = XY plot label = 0 # Labels on wiggle tracks are redundant. [CoverageDensity] feature = coverage:10000 glyph = wiggle_density height = 30 bgcolor = gray bicolor_pivot = 10 pos_color = blue neg_color = red key = Density label = 0 # labels on wiggle tracks are redundant Here is a URL to see what is displayed: http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/jamesbam/ Wes Barris wrote: > Scott Cain wrote: >> Hi Wes, >> >> Attached are the two conf files that I used to create the poster for >> GBrowse 1.70 (I think I really used 1.71b from svn, but that shouldn't >> matter, but you do need to get Bio-DB-Sam from svn). Let me know if >> you have any questions. > > Hi Scott, > > I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without > the curses or zlib libraries because I am not trying to use it to > create .bam files or to use the samtools tview option). I just did > an svn checkout of Bio-Samtools and built and installed that. Here > are portions of my .conf file: > > [GENERAL] > description = MrsFast > db_adaptor = Bio::DB::Sam > db_args = -bam /work/bs/tmp/hmgu_080725_HWI-EAS186_307FYAAXX_1.sorted.bam > > [Match] > feature = match > glyph = segments > bgcolor = blue > fgcolor = blue > height = 3 > label = sub {shift->display_name} > label density = 50 > bump = fast > key = BAM Alignments > > [CoverageXyplot] > feature = coverage:10000 > glyph = wiggle_xyplot > height = 50 > fgcolor = black > bicolor_pivot = 20 > pos_color = blue > neg_color = red > key = XY plot > label = 0 # Labels on wiggle tracks are redundant. > > The "Match" stanza works. I can see the individual reads displayed > in GBrowse. However, the coverage plot shows an empty xy plot in > GBrowse. There are no errors in my apache error log file. > > What else could I be missing? > >> Scott >> >> >> On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> wrote: >>> Hi, >>> >>> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) >>> suggests that Gbrowse 1.7 can be used to display coverage density >>> and XY plots from .bam (SamTools) files. >>> >>> I am familiar with samtools. I have .bam files and have created >>> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can successfully >>> display the individual reads using a stanza that includes: >>> >>> feature = match >>> glyph = segments >>> >>> My question is: "How can I display coverage density and XY plots >>> from the .bam file?" I found the following stanza in a previous >>> post but I don't have an explanation of the "feature" or "database" >>> lines: >>> >>> [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) >>> label = 0 # Labels on wiggle tracks are redundant. >>> >>> Can someone provide me with a sample stanza for gbrowse 1.7? >>> -- >>> Wes Barris <wes.barris@...> >>> >>> ------------------------------------------------------------------------------ >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >>> trial. Simplify your report design, integration and deployment - and focus on >>> what you do best, core application coding. Discover what's new with >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> > > -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [ExternalEmail] Re: Bio-SamTools and Gbrowse1.7
by Scott Cain-4
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Hi Wes,
I don't know what to tell you; that is exactly the same set up as I am using (I updated Bio-Samtools from svn today just to make sure there were no changes), and it works for me. Anybody else? Scott On Nov 12, 2009, at 6:39 PM, Wes Barris wrote: > I'm not sure why but I don't seem to be getting any responses to my > question about getting Bio-Samtools to work so I'll try again... > > I am running Gbrowse 1.71b, Bio-Samtools from svn, samtools-0.1.6, > and Bio-Graphics 1.982. > I have a .bam file from which I would like to view alignments, > coverage > density and a coverage XY plot. Gbrowse displays the alignment but > does not display either the density or XY plot. I am assuming that > since the alignments are being displayed that the data is being read > properly from the .bam file. I can't figure out why the wiggle tracks > do not display any data. > > Here are my track definitions (the first of which works): > > [Match] > feature = match > glyph = segments > bgcolor = blue > fgcolor = blue > height = 3 > label = sub {shift->display_name} > label density = 50 > bump = fast > key = BAM Alignments > > [CoverageXyplot] > feature = coverage:10000 > glyph = wiggle_xyplot > height = 50 > fgcolor = black > bicolor_pivot = 20 > pos_color = blue > neg_color = red > key = XY plot > label = 0 # Labels on wiggle tracks are redundant. > > [CoverageDensity] > feature = coverage:10000 > glyph = wiggle_density > height = 30 > bgcolor = gray > bicolor_pivot = 10 > pos_color = blue > neg_color = red > key = Density > label = 0 # labels on wiggle tracks are redundant > > Here is a URL to see what is displayed: > > http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/jamesbam/ > > > > Wes Barris wrote: >> Scott Cain wrote: >>> Hi Wes, >>> >>> Attached are the two conf files that I used to create the poster for >>> GBrowse 1.70 (I think I really used 1.71b from svn, but that >>> shouldn't >>> matter, but you do need to get Bio-DB-Sam from svn). Let me know if >>> you have any questions. >> Hi Scott, >> I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without >> the curses or zlib libraries because I am not trying to use it to >> create .bam files or to use the samtools tview option). I just did >> an svn checkout of Bio-Samtools and built and installed that. Here >> are portions of my .conf file: >> [GENERAL] >> description = MrsFast >> db_adaptor = Bio::DB::Sam >> db_args = -bam /work/bs/tmp/hmgu_080725_HWI- >> EAS186_307FYAAXX_1.sorted.bam >> [Match] >> feature = match >> glyph = segments >> bgcolor = blue >> fgcolor = blue >> height = 3 >> label = sub {shift->display_name} >> label density = 50 >> bump = fast >> key = BAM Alignments >> [CoverageXyplot] >> feature = coverage:10000 >> glyph = wiggle_xyplot >> height = 50 >> fgcolor = black >> bicolor_pivot = 20 >> pos_color = blue >> neg_color = red >> key = XY plot >> label = 0 # Labels on wiggle tracks are redundant. >> The "Match" stanza works. I can see the individual reads displayed >> in GBrowse. However, the coverage plot shows an empty xy plot in >> GBrowse. There are no errors in my apache error log file. >> What else could I be missing? >>> Scott >>> >>> >>> On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> >>> wrote: >>>> Hi, >>>> >>>> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) >>>> suggests that Gbrowse 1.7 can be used to display coverage density >>>> and XY plots from .bam (SamTools) files. >>>> >>>> I am familiar with samtools. I have .bam files and have created >>>> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can >>>> successfully >>>> display the individual reads using a stanza that includes: >>>> >>>> feature = match >>>> glyph = segments >>>> >>>> My question is: "How can I display coverage density and XY plots >>>> from the .bam file?" I found the following stanza in a previous >>>> post but I don't have an explanation of the "feature" or "database" >>>> lines: >>>> >>>> [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) >>>> label = 0 # Labels on wiggle tracks are redundant. >>>> >>>> Can someone provide me with a sample stanza for gbrowse 1.7? >>>> -- >>>> Wes Barris <wes.barris@...> >>>> >>>> ------------------------------------------------------------------------------ >>>> Let Crystal Reports handle the reporting - Free Crystal Reports >>>> 2008 30-Day >>>> trial. Simplify your report design, integration and deployment - >>>> and focus on >>>> what you do best, core application coding. Discover what's new with >>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>> >>> > > > -- > Wes Barris <wes.barris@...> ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [ExternalEmail] Re: Bio-SamTools and Gbrowse1.7
by Wes Barris
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Scott Cain wrote:
> Hi Wes, > > I don't know what to tell you; that is exactly the same set up as I am > using (I updated Bio-Samtools from svn today just to make sure there > were no changes), and it works for me. > > Anybody else? I've reinstalled Bio-Graphics-1.982. I've reinstalled the latest (svn) gbrowse 1.7 I'm using Scott's sample ecolisam.conf file with only the -bam and -fasta locations changed. I'm using the samtools-0.1.6/example/ex1.bam file. Still, I get no data showing in the wiggle tracks (data does show in the alignment track). I'm wondering if there is some old stuff in my perl5 tree that might be causing problems. Are there supposed to be multiple Wiggle.pm files? wes@bioweb> find /usr/lib/perl5 -name "Wiggle*" -print /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle.pm /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Wiggle.pm /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Wiggle /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/WiggleBlockFile.pm Some of this might be left over from older versions of Bio-Graphics/bioperl. However, I'm not sure how to uninstall an old perl module. Could someone with a working samtools/wiggle density/coverage plot check to see if they have the same Wiggle* files in their perl5 tree? > Scott > > > > On Nov 12, 2009, at 6:39 PM, Wes Barris wrote: > >> I'm not sure why but I don't seem to be getting any responses to my >> question about getting Bio-Samtools to work so I'll try again... >> >> I am running Gbrowse 1.71b, Bio-Samtools from svn, samtools-0.1.6, >> and Bio-Graphics 1.982. >> I have a .bam file from which I would like to view alignments, >> coverage >> density and a coverage XY plot. Gbrowse displays the alignment but >> does not display either the density or XY plot. I am assuming that >> since the alignments are being displayed that the data is being read >> properly from the .bam file. I can't figure out why the wiggle tracks >> do not display any data. >> >> Here are my track definitions (the first of which works): >> >> [Match] >> feature = match >> glyph = segments >> bgcolor = blue >> fgcolor = blue >> height = 3 >> label = sub {shift->display_name} >> label density = 50 >> bump = fast >> key = BAM Alignments >> >> [CoverageXyplot] >> feature = coverage:10000 >> glyph = wiggle_xyplot >> height = 50 >> fgcolor = black >> bicolor_pivot = 20 >> pos_color = blue >> neg_color = red >> key = XY plot >> label = 0 # Labels on wiggle tracks are redundant. >> >> [CoverageDensity] >> feature = coverage:10000 >> glyph = wiggle_density >> height = 30 >> bgcolor = gray >> bicolor_pivot = 10 >> pos_color = blue >> neg_color = red >> key = Density >> label = 0 # labels on wiggle tracks are redundant >> >> Here is a URL to see what is displayed: >> >> http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/jamesbam/ >> >> >> >> Wes Barris wrote: >>> Scott Cain wrote: >>>> Hi Wes, >>>> >>>> Attached are the two conf files that I used to create the poster for >>>> GBrowse 1.70 (I think I really used 1.71b from svn, but that >>>> shouldn't >>>> matter, but you do need to get Bio-DB-Sam from svn). Let me know if >>>> you have any questions. >>> Hi Scott, >>> I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without >>> the curses or zlib libraries because I am not trying to use it to >>> create .bam files or to use the samtools tview option). I just did >>> an svn checkout of Bio-Samtools and built and installed that. Here >>> are portions of my .conf file: >>> [GENERAL] >>> description = MrsFast >>> db_adaptor = Bio::DB::Sam >>> db_args = -bam /work/bs/tmp/hmgu_080725_HWI- >>> EAS186_307FYAAXX_1.sorted.bam >>> [Match] >>> feature = match >>> glyph = segments >>> bgcolor = blue >>> fgcolor = blue >>> height = 3 >>> label = sub {shift->display_name} >>> label density = 50 >>> bump = fast >>> key = BAM Alignments >>> [CoverageXyplot] >>> feature = coverage:10000 >>> glyph = wiggle_xyplot >>> height = 50 >>> fgcolor = black >>> bicolor_pivot = 20 >>> pos_color = blue >>> neg_color = red >>> key = XY plot >>> label = 0 # Labels on wiggle tracks are redundant. >>> The "Match" stanza works. I can see the individual reads displayed >>> in GBrowse. However, the coverage plot shows an empty xy plot in >>> GBrowse. There are no errors in my apache error log file. >>> What else could I be missing? >>>> Scott >>>> >>>> >>>> On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> >>>> wrote: >>>>> Hi, >>>>> >>>>> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) >>>>> suggests that Gbrowse 1.7 can be used to display coverage density >>>>> and XY plots from .bam (SamTools) files. >>>>> >>>>> I am familiar with samtools. I have .bam files and have created >>>>> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can >>>>> successfully >>>>> display the individual reads using a stanza that includes: >>>>> >>>>> feature = match >>>>> glyph = segments >>>>> >>>>> My question is: "How can I display coverage density and XY plots >>>>> from the .bam file?" I found the following stanza in a previous >>>>> post but I don't have an explanation of the "feature" or "database" >>>>> lines: >>>>> >>>>> [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) >>>>> label = 0 # Labels on wiggle tracks are redundant. >>>>> >>>>> Can someone provide me with a sample stanza for gbrowse 1.7? >>>>> -- >>>>> Wes Barris <wes.barris@...> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Let Crystal Reports handle the reporting - Free Crystal Reports >>>>> 2008 30-Day >>>>> trial. Simplify your report design, integration and deployment - >>>>> and focus on >>>>> what you do best, core application coding. Discover what's new with >>>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >> >> -- >> Wes Barris <wes.barris@...> > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [ExternalEmail] Re: Bio-SamTools and Gbrowse1.7
by Scott Cain-4
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Hi Wes,
That absolutely could be the problem: I only have the /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle.pm perl module, and the architecture dependent one is old, and complicating matters, is probably preferentially used over the right one (I think the arch directories appear before the others in @INC). I think deleting the offending Graphics directory should do the trick, though you may need to reinstall Bio::Graphics after doing so, in case the current Bio::Graphics puts stuff in the arch-dep directories (I don't think it does, but it's possible). Scott On Mon, Nov 16, 2009 at 12:07 AM, Wes Barris <wes.barris@...> wrote: > Scott Cain wrote: >> >> Hi Wes, >> >> I don't know what to tell you; that is exactly the same set up as I am >> using (I updated Bio-Samtools from svn today just to make sure there were >> no changes), and it works for me. >> >> Anybody else? > > I've reinstalled Bio-Graphics-1.982. > I've reinstalled the latest (svn) gbrowse 1.7 > I'm using Scott's sample ecolisam.conf file with only the -bam and > -fasta locations changed. > I'm using the samtools-0.1.6/example/ex1.bam file. > > Still, I get no data showing in the wiggle tracks (data does show > in the alignment track). > > I'm wondering if there is some old stuff in my perl5 tree that might > be causing problems. Are there supposed to be multiple Wiggle.pm files? > > wes@bioweb> find /usr/lib/perl5 -name "Wiggle*" -print > /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle.pm > /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Wiggle.pm > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Wiggle > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/WiggleBlockFile.pm > > Some of this might be left over from older versions of > Bio-Graphics/bioperl. However, I'm not sure how to uninstall > an old perl module. > > Could someone with a working samtools/wiggle density/coverage plot > check to see if they have the same Wiggle* files in their perl5 tree? > > >> Scott >> >> >> >> On Nov 12, 2009, at 6:39 PM, Wes Barris wrote: >> >>> I'm not sure why but I don't seem to be getting any responses to my >>> question about getting Bio-Samtools to work so I'll try again... >>> >>> I am running Gbrowse 1.71b, Bio-Samtools from svn, samtools-0.1.6, >>> and Bio-Graphics 1.982. >>> I have a .bam file from which I would like to view alignments, coverage >>> density and a coverage XY plot. Gbrowse displays the alignment but >>> does not display either the density or XY plot. I am assuming that >>> since the alignments are being displayed that the data is being read >>> properly from the .bam file. I can't figure out why the wiggle tracks >>> do not display any data. >>> >>> Here are my track definitions (the first of which works): >>> >>> [Match] >>> feature = match >>> glyph = segments >>> bgcolor = blue >>> fgcolor = blue >>> height = 3 >>> label = sub {shift->display_name} >>> label density = 50 >>> bump = fast >>> key = BAM Alignments >>> >>> [CoverageXyplot] >>> feature = coverage:10000 >>> glyph = wiggle_xyplot >>> height = 50 >>> fgcolor = black >>> bicolor_pivot = 20 >>> pos_color = blue >>> neg_color = red >>> key = XY plot >>> label = 0 # Labels on wiggle tracks are redundant. >>> >>> [CoverageDensity] >>> feature = coverage:10000 >>> glyph = wiggle_density >>> height = 30 >>> bgcolor = gray >>> bicolor_pivot = 10 >>> pos_color = blue >>> neg_color = red >>> key = Density >>> label = 0 # labels on wiggle tracks are redundant >>> >>> Here is a URL to see what is displayed: >>> >>> http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/jamesbam/ >>> >>> >>> >>> Wes Barris wrote: >>>> >>>> Scott Cain wrote: >>>>> >>>>> Hi Wes, >>>>> >>>>> Attached are the two conf files that I used to create the poster for >>>>> GBrowse 1.70 (I think I really used 1.71b from svn, but that shouldn't >>>>> matter, but you do need to get Bio-DB-Sam from svn). Let me know if >>>>> you have any questions. >>>> >>>> Hi Scott, >>>> I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without >>>> the curses or zlib libraries because I am not trying to use it to >>>> create .bam files or to use the samtools tview option). I just did >>>> an svn checkout of Bio-Samtools and built and installed that. Here >>>> are portions of my .conf file: >>>> [GENERAL] >>>> description = MrsFast >>>> db_adaptor = Bio::DB::Sam >>>> db_args = -bam /work/bs/tmp/hmgu_080725_HWI- >>>> EAS186_307FYAAXX_1.sorted.bam >>>> [Match] >>>> feature = match >>>> glyph = segments >>>> bgcolor = blue >>>> fgcolor = blue >>>> height = 3 >>>> label = sub {shift->display_name} >>>> label density = 50 >>>> bump = fast >>>> key = BAM Alignments >>>> [CoverageXyplot] >>>> feature = coverage:10000 >>>> glyph = wiggle_xyplot >>>> height = 50 >>>> fgcolor = black >>>> bicolor_pivot = 20 >>>> pos_color = blue >>>> neg_color = red >>>> key = XY plot >>>> label = 0 # Labels on wiggle tracks are redundant. >>>> The "Match" stanza works. I can see the individual reads displayed >>>> in GBrowse. However, the coverage plot shows an empty xy plot in >>>> GBrowse. There are no errors in my apache error log file. >>>> What else could I be missing? >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> >>>>> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) >>>>>> suggests that Gbrowse 1.7 can be used to display coverage density >>>>>> and XY plots from .bam (SamTools) files. >>>>>> >>>>>> I am familiar with samtools. I have .bam files and have created >>>>>> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can >>>>>> successfully >>>>>> display the individual reads using a stanza that includes: >>>>>> >>>>>> feature = match >>>>>> glyph = segments >>>>>> >>>>>> My question is: "How can I display coverage density and XY plots >>>>>> from the .bam file?" I found the following stanza in a previous >>>>>> post but I don't have an explanation of the "feature" or "database" >>>>>> lines: >>>>>> >>>>>> [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) >>>>>> label = 0 # Labels on wiggle tracks are redundant. >>>>>> >>>>>> Can someone provide me with a sample stanza for gbrowse 1.7? >>>>>> -- >>>>>> Wes Barris <wes.barris@...> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>>>>> 30-Day >>>>>> trial. Simplify your report design, integration and deployment - and >>>>>> focus on >>>>>> what you do best, core application coding. Discover what's new with >>>>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>> >>> >>> -- >>> Wes Barris <wes.barris@...> >> >> ----------------------------------------------------------------------- >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> >> > > > -- > Wes Barris <wes.barris@...> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Bio-SamTools and Gbrowse1.7
by Lincoln Stein-3
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You'll need a recent checkout of Bio::Graphics (or the version on CPAN).
Lincoln On Tue, Nov 10, 2009 at 6:50 PM, Wes Barris <wes.barris@...> wrote:
-- 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@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Bio-SamTools and Gbrowse1.7
by Wes Barris
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Lincoln Stein wrote:
> You'll need a recent checkout of Bio::Graphics (or the version on CPAN). For gbrowse-1.71b should I be using Bio-Graphics-1.982 or Bio-Graphics-1.991? > Lincoln > > On Tue, Nov 10, 2009 at 6:50 PM, Wes Barris <wes.barris@...> wrote: > > Scott Cain wrote: > > Hi Wes, > > > > Attached are the two conf files that I used to create the poster for > > GBrowse 1.70 (I think I really used 1.71b from svn, but that > shouldn't > > matter, but you do need to get Bio-DB-Sam from svn). Let me know if > > you have any questions. > > Hi Scott, > > I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without > the curses or zlib libraries because I am not trying to use it to > create .bam files or to use the samtools tview option). I just did > an svn checkout of Bio-Samtools and built and installed that. Here > are portions of my .conf file: > > [GENERAL] > description = MrsFast > db_adaptor = Bio::DB::Sam > db_args = -bam > /work/bs/tmp/hmgu_080725_HWI-EAS186_307FYAAXX_1.sorted.bam > > [Match] > feature = match > glyph = segments > bgcolor = blue > fgcolor = blue > height = 3 > label = sub {shift->display_name} > label density = 50 > bump = fast > key = BAM Alignments > > [CoverageXyplot] > feature = coverage:10000 > glyph = wiggle_xyplot > height = 50 > fgcolor = black > bicolor_pivot = 20 > pos_color = blue > neg_color = red > key = XY plot > label = 0 # Labels on wiggle tracks are redundant. > > The "Match" stanza works. I can see the individual reads displayed > in GBrowse. However, the coverage plot shows an empty xy plot in > GBrowse. There are no errors in my apache error log file. > > What else could I be missing? > > > Scott > > > > > > On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> > wrote: > >> Hi, > >> > >> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) > >> suggests that Gbrowse 1.7 can be used to display coverage density > >> and XY plots from .bam (SamTools) files. > >> > >> I am familiar with samtools. I have .bam files and have created > >> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can > successfully > >> display the individual reads using a stanza that includes: > >> > >> feature = match > >> glyph = segments > >> > >> My question is: "How can I display coverage density and XY plots > >> from the .bam file?" I found the following stanza in a previous > >> post but I don't have an explanation of the "feature" or "database" > >> lines: > >> > >> [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) > >> label = 0 # Labels on wiggle tracks are redundant. > >> > >> Can someone provide me with a sample stanza for gbrowse 1.7? > >> -- > >> Wes Barris <wes.barris@...> > >> > >> > ------------------------------------------------------------------------------ > >> Let Crystal Reports handle the reporting - Free Crystal Reports > 2008 30-Day > >> trial. Simplify your report design, integration and deployment - > and focus on > >> what you do best, core application coding. Discover what's new with > >> Crystal Reports now. http://p.sf.net/sfu/bobj-july > >> _______________________________________________ > >> Gmod-gbrowse mailing list > >> Gmod-gbrowse@... > <mailto:Gmod-gbrowse@...> > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > >> > > > > > > > > > -- > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > <mailto:Gmod-gbrowse@...> > 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@... > <mailto:Renata.Musa@...>> -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [ExternalEmail] Re: Bio-SamTools and Gbrowse1.7
by Wes Barris
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Scott Cain wrote:
> Hi Wes, > > That absolutely could be the problem: I only have the > /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle.pm perl module, and > the architecture dependent one is old, and complicating matters, is > probably preferentially used over the right one (I think the arch > directories appear before the others in @INC). > > I think deleting the offending Graphics directory should do the trick, > though you may need to reinstall Bio::Graphics after doing so, in case > the current Bio::Graphics puts stuff in the arch-dep directories (I > don't think it does, but it's possible). I finally got wiggle tracks to display from .bam files. Deleting the offending Wiggle*.pm files had a cascading affect on reinstalling software (Bio-Graphics, Bio-Perl, Gbrowse) but I finally got things working again. Thanks for your help. > Scott > > > > On Mon, Nov 16, 2009 at 12:07 AM, Wes Barris <wes.barris@...> wrote: >> Scott Cain wrote: >>> Hi Wes, >>> >>> I don't know what to tell you; that is exactly the same set up as I am >>> using (I updated Bio-Samtools from svn today just to make sure there were >>> no changes), and it works for me. >>> >>> Anybody else? >> I've reinstalled Bio-Graphics-1.982. >> I've reinstalled the latest (svn) gbrowse 1.7 >> I'm using Scott's sample ecolisam.conf file with only the -bam and >> -fasta locations changed. >> I'm using the samtools-0.1.6/example/ex1.bam file. >> >> Still, I get no data showing in the wiggle tracks (data does show >> in the alignment track). >> >> I'm wondering if there is some old stuff in my perl5 tree that might >> be causing problems. Are there supposed to be multiple Wiggle.pm files? >> >> wes@bioweb> find /usr/lib/perl5 -name "Wiggle*" -print >> /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle.pm >> /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Wiggle >> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Wiggle.pm >> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/Wiggle >> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi/Bio/Graphics/WiggleBlockFile.pm >> >> Some of this might be left over from older versions of >> Bio-Graphics/bioperl. However, I'm not sure how to uninstall >> an old perl module. >> >> Could someone with a working samtools/wiggle density/coverage plot >> check to see if they have the same Wiggle* files in their perl5 tree? >> >> >>> Scott >>> >>> >>> >>> On Nov 12, 2009, at 6:39 PM, Wes Barris wrote: >>> >>>> I'm not sure why but I don't seem to be getting any responses to my >>>> question about getting Bio-Samtools to work so I'll try again... >>>> >>>> I am running Gbrowse 1.71b, Bio-Samtools from svn, samtools-0.1.6, >>>> and Bio-Graphics 1.982. >>>> I have a .bam file from which I would like to view alignments, coverage >>>> density and a coverage XY plot. Gbrowse displays the alignment but >>>> does not display either the density or XY plot. I am assuming that >>>> since the alignments are being displayed that the data is being read >>>> properly from the .bam file. I can't figure out why the wiggle tracks >>>> do not display any data. >>>> >>>> Here are my track definitions (the first of which works): >>>> >>>> [Match] >>>> feature = match >>>> glyph = segments >>>> bgcolor = blue >>>> fgcolor = blue >>>> height = 3 >>>> label = sub {shift->display_name} >>>> label density = 50 >>>> bump = fast >>>> key = BAM Alignments >>>> >>>> [CoverageXyplot] >>>> feature = coverage:10000 >>>> glyph = wiggle_xyplot >>>> height = 50 >>>> fgcolor = black >>>> bicolor_pivot = 20 >>>> pos_color = blue >>>> neg_color = red >>>> key = XY plot >>>> label = 0 # Labels on wiggle tracks are redundant. >>>> >>>> [CoverageDensity] >>>> feature = coverage:10000 >>>> glyph = wiggle_density >>>> height = 30 >>>> bgcolor = gray >>>> bicolor_pivot = 10 >>>> pos_color = blue >>>> neg_color = red >>>> key = Density >>>> label = 0 # labels on wiggle tracks are redundant >>>> >>>> Here is a URL to see what is displayed: >>>> >>>> http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/jamesbam/ >>>> >>>> >>>> >>>> Wes Barris wrote: >>>>> Scott Cain wrote: >>>>>> Hi Wes, >>>>>> >>>>>> Attached are the two conf files that I used to create the poster for >>>>>> GBrowse 1.70 (I think I really used 1.71b from svn, but that shouldn't >>>>>> matter, but you do need to get Bio-DB-Sam from svn). Let me know if >>>>>> you have any questions. >>>>> Hi Scott, >>>>> I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without >>>>> the curses or zlib libraries because I am not trying to use it to >>>>> create .bam files or to use the samtools tview option). I just did >>>>> an svn checkout of Bio-Samtools and built and installed that. Here >>>>> are portions of my .conf file: >>>>> [GENERAL] >>>>> description = MrsFast >>>>> db_adaptor = Bio::DB::Sam >>>>> db_args = -bam /work/bs/tmp/hmgu_080725_HWI- >>>>> EAS186_307FYAAXX_1.sorted.bam >>>>> [Match] >>>>> feature = match >>>>> glyph = segments >>>>> bgcolor = blue >>>>> fgcolor = blue >>>>> height = 3 >>>>> label = sub {shift->display_name} >>>>> label density = 50 >>>>> bump = fast >>>>> key = BAM Alignments >>>>> [CoverageXyplot] >>>>> feature = coverage:10000 >>>>> glyph = wiggle_xyplot >>>>> height = 50 >>>>> fgcolor = black >>>>> bicolor_pivot = 20 >>>>> pos_color = blue >>>>> neg_color = red >>>>> key = XY plot >>>>> label = 0 # Labels on wiggle tracks are redundant. >>>>> The "Match" stanza works. I can see the individual reads displayed >>>>> in GBrowse. However, the coverage plot shows an empty xy plot in >>>>> GBrowse. There are no errors in my apache error log file. >>>>> What else could I be missing? >>>>>> Scott >>>>>> >>>>>> >>>>>> On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> >>>>>> wrote: >>>>>>> Hi, >>>>>>> >>>>>>> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf) >>>>>>> suggests that Gbrowse 1.7 can be used to display coverage density >>>>>>> and XY plots from .bam (SamTools) files. >>>>>>> >>>>>>> I am familiar with samtools. I have .bam files and have created >>>>>>> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can >>>>>>> successfully >>>>>>> display the individual reads using a stanza that includes: >>>>>>> >>>>>>> feature = match >>>>>>> glyph = segments >>>>>>> >>>>>>> My question is: "How can I display coverage density and XY plots >>>>>>> from the .bam file?" I found the following stanza in a previous >>>>>>> post but I don't have an explanation of the "feature" or "database" >>>>>>> lines: >>>>>>> >>>>>>> [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) >>>>>>> label = 0 # Labels on wiggle tracks are redundant. >>>>>>> >>>>>>> Can someone provide me with a sample stanza for gbrowse 1.7? >>>>>>> -- >>>>>>> Wes Barris <wes.barris@...> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>>>>>> 30-Day >>>>>>> trial. Simplify your report design, integration and deployment - and >>>>>>> focus on >>>>>>> what you do best, core application coding. Discover what's new with >>>>>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse@... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>> -- >>>> Wes Barris <wes.barris@...> >>> ----------------------------------------------------------------------- >>> Scott Cain, Ph. D. scott at scottcain dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >>> >>> >>> >> >> -- >> Wes Barris <wes.barris@...> >> > > > -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Bio-SamTools and Gbrowse1.7
by Lincoln Stein-3
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Hi Wes,
The latest Bio::Graphics is always best. They are not tied to any specific revisions of GBrowse. Best, Lincoln On Mon, Nov 16, 2009 at 6:04 PM, Wes Barris <wes.barris@...> wrote:
-- 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@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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