how to display multiple tracks of read data in terms of coverage plots
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I can display one track use samtools according to the NGS tutorial.
but I want to display multiple tracks, I don't know how to set the .conf file. the single track .conf file is: [GENERAL] description = test2 one contig database = test2 ...... [test2:database] db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam search options = default ...... [CoverageXyplot] feature = coverage glyph = wiggle_xyplot database = test2 height = 50 fgcolor = black bicolor_pivot = 20 pos_color = blue neg_color = red key = Coverage (xyplot) category = Reads label = 0 # Labels on wiggle tracks are redundant. ---------------------------- if I have multiple .bam files need to display multiple tracks (not subtracks), I don't know how to set the .conf file. any ideas, thanks, |
Re: how to display multiple tracks of read data in terms of coverage plots
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On 2/08/2010 6:56 AM, neil wrote:
> > I can display one track use samtools according to the NGS tutorial. > but I want to display multiple tracks, I don't know how to set the .conf > file. Hi Neil, For multiple .bam files you would declare multiple databases each pointing to their respective .bam file. Then you would have two separate track definitions (READS, XYplot, etc.) each pointing to their respective database definition. > the single track .conf file is: > > > [GENERAL] > description = test2 one contig > database = test2 > ...... > > [test2:database] > db_adaptor = Bio::DB::Sam > db_args = -fasta > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa > -bam > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam > search options = default > > ...... > > [CoverageXyplot] > feature = coverage > glyph = wiggle_xyplot > database = test2 > height = 50 > fgcolor = black > bicolor_pivot = 20 > pos_color = blue > neg_color = red > key = Coverage (xyplot) > category = Reads > label = 0 # Labels on wiggle tracks are redundant. > > > ---------------------------- > > if I have multiple .bam files need to display multiple tracks (not > subtracks), I don't know how to set the .conf file. > > any ideas, > > thanks, > > > > > > > -- Wes Barris ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Hi Wes,
thanks,
You mean I should declare multiple databases.
but do I have to copy the same .fa file to each databases? like:
[test2:database]
db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam search options = default [test3:database]
db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test3.bam search options = default ....................
can you send me one copy of the .conf file you introduced ?
thanks,
On Sun, Aug 1, 2010 at 9:44 PM, Wes Barris [via Generic Model Organism System Database] <[hidden email]> wrote: On 2/08/2010 6:56 AM, neil wrote: |
Re: how to display multiple tracks of read data in terms of coverage plots
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In reply to this post by neil
Provided you have valid MD tags on each record you don't need the .fa file. You can use
samtools calms To generate them if missing. Regards, Keiran Sent from my HTC Magic Android phone. -----Original Message----- From: neil [[hidden email]] Received: 02/08/2010 14:35 To: [hidden email] [[hidden email]] Subject: Re: [Gmod-gbrowse] how to display multiple tracks of read data in terms of coverage plots Hi Wes, thanks, You mean I should declare multiple databases. but do I have to copy the same .fa file to each databases? like: [test2:database] db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam search options = default [test3:database] db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test3.bam search options = default .................... can you send me one copy of the .conf file you introduced ? thanks, On Sun, Aug 1, 2010 at 9:44 PM, Wes Barris [via Generic Model Organism System Database] <[hidden email]<ml-node%[hidden email]> > wrote: > On 2/08/2010 6:56 AM, neil wrote: > > > > I can display one track use samtools according to the NGS tutorial. > > but I want to display multiple tracks, I don't know how to set the .conf > > file. > > Hi Neil, > > For multiple .bam files you would declare multiple databases each pointing > to their respective .bam file. Then you would have two separate track > definitions (READS, XYplot, etc.) each pointing to their respective > database definition. > > > the single track .conf file is: > > > > > > [GENERAL] > > description = test2 one contig > > database = test2 > > ...... > > > > [test2:database] > > db_adaptor = Bio::DB::Sam > > db_args = -fasta > > > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa > > > -bam > > > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam > > > search options = default > > > > ...... > > > > [CoverageXyplot] > > feature = coverage > > glyph = wiggle_xyplot > > database = test2 > > height = 50 > > fgcolor = black > > bicolor_pivot = 20 > > pos_color = blue > > neg_color = red > > key = Coverage (xyplot) > > category = Reads > > label = 0 # Labels on wiggle tracks are redundant. > > > > > > ---------------------------- > > > > if I have multiple .bam files need to display multiple tracks (not > > subtracks), I don't know how to set the .conf file. > > > > any ideas, > > > > thanks, > > > > > > > > > > > > > > > > > -- > Wes Barris > > ------------------------------------------------------------------------------ > > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Gmod-gbrowse mailing list > [hidden email] <http://user/SendEmail.jtp?type=node&node=2261335&i=0> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > ------------------------------ > View message @ > http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261335.html > To unsubscribe from how to display multiple tracks of read data in terms of > coverage plots, click here<http://generic-model-organism-system-database.450254.n5.nabble.com/subscriptions/Unsubscribe.jtp?code=bmVpbG5pdS5jbkBnbWFpbC5jb218MjI2MTIxOXwtMTM0NDI4MTIzNA==>. > > > View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261408.html Sent from the gmod-gbrowse mailing list archive at Nabble.com. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: how to display multiple tracks of read data in terms of coverage plots
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sorry thats:
samtools calmd Your config would look something like this if you have MD populated/available: [mt_wg_bam:database] db_adaptor = Bio::DB::Sam db_args = -bam '/nfs/cancer_ref01/gbrowse/pipeline_conf/databases/HUMAN_37/HCC1187a50/wg_mt.bam' -split_splices 1 search options = none You also have the option of getting the fasta sequence from a DB if you are using one: [normalsam:database] db_adaptor = Bio::DB::Sam db_args = sub { require Bio::DB::SeqFeature::Store; ( -fasta => Bio::DB::SeqFeature::Store->new(-adaptor=>'DBI::mysql',-dsn=>'GRC37_56',-user =>'nobody'), -bam => '/var/tmp/gBrowse_data/databases/PD2125/bam/PD2125b.bam' ) } search options = none Regards, Keiran Raine Senior Computer Biologist The Cancer Genome Project Ext: 7703 [hidden email] On 2 Aug 2010, at 15:06, Keiran Raine wrote: Provided you have valid MD tags on each record you don't need the .fa file. You can use samtools calms To generate them if missing. Regards, Keiran Sent from my HTC Magic Android phone. -----Original Message----- From: neil [[hidden email]] Received: 02/08/2010 14:35 To: [hidden email] [[hidden email]] Subject: Re: [Gmod-gbrowse] how to display multiple tracks of read data in terms of coverage plots Hi Wes, thanks, You mean I should declare multiple databases. but do I have to copy the same .fa file to each databases? like: [test2:database] db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam search options = default [test3:database] db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test3.bam search options = default .................... can you send me one copy of the .conf file you introduced ? thanks, On Sun, Aug 1, 2010 at 9:44 PM, Wes Barris [via Generic Model Organism System Database] <[hidden email]<ml-node%[hidden email]> wrote: On 2/08/2010 6:56 AM, neil wrote: I can display one track use samtools according to the NGS tutorial. but I want to display multiple tracks, I don't know how to set the .conf file. Hi Neil, For multiple .bam files you would declare multiple databases each pointing to their respective .bam file. Then you would have two separate track definitions (READS, XYplot, etc.) each pointing to their respective database definition. the single track .conf file is: [GENERAL] description = test2 one contig database = test2 ...... [test2:database] db_adaptor = Bio::DB::Sam db_args = -fasta /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa -bam /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam search options = default ...... [CoverageXyplot] feature = coverage glyph = wiggle_xyplot database = test2 height = 50 fgcolor = black bicolor_pivot = 20 pos_color = blue neg_color = red key = Coverage (xyplot) category = Reads label = 0 # Labels on wiggle tracks are redundant. ---------------------------- if I have multiple .bam files need to display multiple tracks (not subtracks), I don't know how to set the .conf file. any ideas, thanks, -- Wes Barris ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Gmod-gbrowse mailing list [hidden email] <http://user/SendEmail.jtp?type=node&node=2261335&i=0> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------ View message @ http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261335.html To unsubscribe from how to display multiple tracks of read data in terms of coverage plots, click here<http://generic-model-organism-system-database.450254.n5.nabble.com/subscriptions/Unsubscribe.jtp?code=bmVpbG5pdS5jbkBnbWFpbC5jb218MjI2MTIxOXwtMTM0NDI4MTIzNA==>. -- View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261408.html Sent from the gmod-gbrowse mailing list archive at Nabble.com. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm_______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: how to display multiple tracks of read data in terms of coverage plots
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In reply to this post by neil
On 2/08/2010 3:27 PM, neil wrote:
> Hi Wes, > thanks, > You mean I should declare multiple databases. Yes. > but do I have to copy the same .fa file to each databases? like: You wouldn't copy the file. If more than one .bam files used the same reference sequence, you would just point the gbrowse database definitions to the same fasta file. > [test2:database] > db_adaptor = Bio::DB::Sam > db_args = -fasta > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa > -bam > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam > search options = default > [test3:database] > db_adaptor = Bio::DB::Sam > db_args = -fasta > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa > -bam > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test3.bam > search options = default > .................... > can you send me one copy of the .conf file you introduced ? All you need to do is duplicate your stanzas giving each a different name and database: [CoverageXyplot1] database = test1 . . . [CoverageXyplot2] database = test2 . . . > thanks, > > > On Sun, Aug 1, 2010 at 9:44 PM, Wes Barris [via Generic Model Organism System Database] <[hidden email] </user/SendEmail.jtp?type=node&node=2261408&i=0>> wrote: > > On 2/08/2010 6:56 AM, neil wrote: > > > > I can display one track use samtools according to the NGS tutorial. > > but I want to display multiple tracks, I don't know how to set the .conf > > file. > > Hi Neil, > > For multiple .bam files you would declare multiple databases each pointing > to their respective .bam file. Then you would have two separate track > definitions (READS, XYplot, etc.) each pointing to their respective > database definition. > > > the single track .conf file is: > > > > > > [GENERAL] > > description = test2 one contig > > database = test2 > > ...... > > > > [test2:database] > > db_adaptor = Bio::DB::Sam > > db_args = -fasta > > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.fa > > -bam > > /home/data/www/home/gbrowse2/apache/htdocs/gbrowse2/databases/test2/test2.bam > > search options = default > > > > ...... > > > > [CoverageXyplot] > > feature = coverage > > glyph = wiggle_xyplot > > database = test2 > > height = 50 > > fgcolor = black > > bicolor_pivot = 20 > > pos_color = blue > > neg_color = red > > key = Coverage (xyplot) > > category = Reads > > label = 0 # Labels on wiggle tracks are redundant. > > > > > > ---------------------------- > > > > if I have multiple .bam files need to display multiple tracks (not > > subtracks), I don't know how to set the .conf file. > > > > any ideas, > > > > thanks, > > > > > > > > > > > > > > > > > -- > Wes Barris > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Gmod-gbrowse mailing list > [hidden email] <http://user/SendEmail.jtp?type=node&node=2261335&i=0> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > View message @ http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261335.html > <http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261335.html?by-user=t> > To unsubscribe from how to display multiple tracks of read data in terms of coverage plots, click here. > > > > -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > View this message in context: Re: how to display multiple tracks of read data in terms of coverage plots > <http://generic-model-organism-system-database.450254.n5.nabble.com/how-to-display-multiple-tracks-of-read-data-in-terms-of-coverage-plots-tp2261219p2261408.html> > Sent from the gmod-gbrowse mailing list archive <http://generic-model-organism-system-database.450254.n5.nabble.com/gmod-gbrowse-f450255.html> at Nabble.com. -- Wes Barris ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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