the problem to show my ChIP-seq data

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the problem to show my ChIP-seq data

neil-2

I want to show my reads to reference genome alignment result like these:
http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png 
(the modENCODE ChIP-seq tracks example)

are there any example config file and GFF file like volvox tutorial example?
so, I can show my dataset follw the exmple.

thanks.
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Re: the problem to show my ChIP-seq data

Adam Witney

Hi Neil,

does this give you what you want?

http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks

You will probably have to upload your data using something like this approach:

http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks

adam


On 26 Jul 2010, at 20:05, neil wrote:

>
> I want to show my reads to reference genome alignment result like these:
> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png 
> (the modENCODE ChIP-seq tracks example)
>
> are there any example config file and GFF file like volvox tutorial example?
> so, I can show my dataset follw the exmple.
>
> thanks.
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
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> 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:
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Re: the problem to show my ChIP-seq data

neil-2
Hi Adam,
 
Thanks.
I just want to get the reads coverage of genome from BLAST results and show like this png graph. it is not ChIP-seq data just 454 reads aligned to reference genome.
 
I don't have to get subtracks and I just want to get one track like this png is ok.
but I don't know how to set config file and GFF file format for this png .
 
thanks again.
 
 


 
On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi Neil,

does this give you what you want?

http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks

You will probably have to upload your data using something like this approach:

http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks

adam


On 26 Jul 2010, at 20:05, neil wrote:

>
> I want to show my reads to reference genome alignment result like these:
> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png 
> (the modENCODE tracks example)
>
> are there any example config file and GFF file like volvox tutorial example?
> so, I can show my dataset follw the exmple.
>
> thanks.
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> 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://ad.doubleclick.net/clk;226879339;13503038;l?
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> Gmod-gbrowse mailing list
> [hidden email]


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Re: the problem to show my ChIP-seq data

Scott Cain
Hi Neil,

So you would like to create a coverage histogram for your blast
results?  Probably the easiest thing to do would be to convert your
blast results to GFF3 using BioPerl's bp_search2gff.pl script and
import that into a Bio::DB::SeqFeature::Store database, and set the
track to show summary information.  That would save you the trouble of
calculating the coverage yourself.  Of course, there are multiple
steps in those few sentences, so I'll let you get started on that and
you can come back here or go to the BioPerl mail list as appropriate
for more detailed questions.

Scott


On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:

> Hi Adam,
>
> Thanks.
> I just want to get the reads coverage of genome from BLAST results and show
> like this png graph. it is not ChIP-seq data just 454 reads aligned to
> reference genome.
> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>
> I don't have to get subtracks and I just want to get one track like this png
> is ok.
> but I don't know how to set config file and GFF file format for this png .
>
> thanks again.
>
>
>
>
> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism
> System Database] <[hidden email]> wrote:
>>
>> Hi Neil,
>>
>> does this give you what you want?
>>
>>
>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>
>> You will probably have to upload your data using something like this
>> approach:
>>
>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>
>> adam
>>
>>
>> On 26 Jul 2010, at 20:05, neil wrote:
>>
>> >
>> > I want to show my reads to reference genome alignment result like these:
>> > http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>> > (the modENCODE tracks example)
>> >
>> > are there any example config file and GFF file like volvox tutorial
>> > example?
>> > so, I can show my dataset follw the exmple.
>> >
>> > thanks.
>> > --
>> > View this message in context:
>> > http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>> > Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > 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:
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>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>> ------------------------------------------------------------------------------
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>> 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:
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>> Gmod-gbrowse mailing list
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>>
>>
>> ________________________________
>> View message @
>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>
>
> ________________________________
> View this message in context: Re: the problem to show my ChIP-seq data
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: the problem to show my ChIP-seq data

J.M.P. Alves
Hi, Scott

Does bp_search2gff.pl accept tabular BLAST results? The documentation is
very sparse on this, but I have tried that and got an empty file:

zcat blastres2_Bc_NO_endo_contigs.fas.gz | bp_search2gff.pl -s TBLASTN
-o BCU_tblastn.gff3 --version 3

Thanks
J

Scott Cain wrote:

> Hi Neil,
>
> So you would like to create a coverage histogram for your blast
> results?  Probably the easiest thing to do would be to convert your
> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
> import that into a Bio::DB::SeqFeature::Store database, and set the
> track to show summary information.  That would save you the trouble of
> calculating the coverage yourself.  Of course, there are multiple
> steps in those few sentences, so I'll let you get started on that and
> you can come back here or go to the BioPerl mail list as appropriate
> for more detailed questions.
>
> Scott
>
>
> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>> Hi Adam,
>>
>> Thanks.
>> I just want to get the reads coverage of genome from BLAST results and show
>> like this png graph. it is not ChIP-seq data just 454 reads aligned to
>> reference genome.
>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>
>> I don't have to get subtracks and I just want to get one track like this png
>> is ok.
>> but I don't know how to set config file and GFF file format for this png .
>>
>> thanks again.
>>
>>
>>
>>
>> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism
>> System Database] <[hidden email]> wrote:
>>> Hi Neil,
>>>
>>> does this give you what you want?
>>>
>>>
>>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>>
>>> You will probably have to upload your data using something like this
>>> approach:
>>>
>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>
>>> adam
>>>
>>>
>>> On 26 Jul 2010, at 20:05, neil wrote:
>>>
>>>> I want to show my reads to reference genome alignment result like these:
>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>> (the modENCODE tracks example)
>>>>
>>>> are there any example config file and GFF file like volvox tutorial
>>>> example?
>>>> so, I can show my dataset follw the exmple.
>>>>
>>>> thanks.
>>>> --
>>>> View this message in context:
>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>> ------------------------------------------------------------------------------
>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>> ________________________________
>>> View message @
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>>
>> ________________________________
>> View this message in context: Re: the problem to show my ChIP-seq data
>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>
>> ------------------------------------------------------------------------------
>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
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>> Gmod-gbrowse mailing list
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>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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Re: the problem to show my ChIP-seq data

Scott Cain
Hi J,

I'm not the author of that tool, but my recollection is that it
supports any format that Bio::SearchIO supports:

         blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)
         fasta      FASTA ‐m9 and ‐m0
         blasttable BLAST ‐m9 or ‐m8 output (both NCBI and WUBLAST tabular)
         megablast  MEGABLAST
         psl        UCSC PSL format
         waba       WABA output
         axt        AXT format
         sim4       Sim4
         hmmer      HMMER hmmpfam and hmmsearch
         exonerate  Exonerate CIGAR and VULGAR format
         blastxml   NCBI BLAST XML
         wise       Genewise ‐genesf format

You have to set the format with a command line flag, eg: -f
blasttable; the default is blast.

Scott


On Tue, Jul 27, 2010 at 2:56 PM, J.M.P. Alves <[hidden email]> wrote:

> Hi, Scott
>
> Does bp_search2gff.pl accept tabular BLAST results? The documentation is
> very sparse on this, but I have tried that and got an empty file:
>
> zcat blastres2_Bc_NO_endo_contigs.fas.gz | bp_search2gff.pl -s TBLASTN -o
> BCU_tblastn.gff3 --version 3
>
> Thanks
> J
>
> Scott Cain wrote:
>>
>> Hi Neil,
>>
>> So you would like to create a coverage histogram for your blast
>> results?  Probably the easiest thing to do would be to convert your
>> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
>> import that into a Bio::DB::SeqFeature::Store database, and set the
>> track to show summary information.  That would save you the trouble of
>> calculating the coverage yourself.  Of course, there are multiple
>> steps in those few sentences, so I'll let you get started on that and
>> you can come back here or go to the BioPerl mail list as appropriate
>> for more detailed questions.
>>
>> Scott
>>
>>
>> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>>>
>>> Hi Adam,
>>>
>>> Thanks.
>>> I just want to get the reads coverage of genome from BLAST results and
>>> show
>>> like this png graph. it is not ChIP-seq data just 454 reads aligned to
>>> reference genome.
>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>
>>> I don't have to get subtracks and I just want to get one track like this
>>> png
>>> is ok.
>>> but I don't know how to set config file and GFF file format for this png
>>> .
>>>
>>> thanks again.
>>>
>>>
>>>
>>>
>>> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism
>>> System Database] <[hidden email]> wrote:
>>>>
>>>> Hi Neil,
>>>>
>>>> does this give you what you want?
>>>>
>>>>
>>>>
>>>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>>>
>>>> You will probably have to upload your data using something like this
>>>> approach:
>>>>
>>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>>
>>>> adam
>>>>
>>>>
>>>> On 26 Jul 2010, at 20:05, neil wrote:
>>>>
>>>>> I want to show my reads to reference genome alignment result like
>>>>> these:
>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>> (the modENCODE tracks example)
>>>>>
>>>>> are there any example config file and GFF file like volvox tutorial
>>>>> example?
>>>>> so, I can show my dataset follw the exmple.
>>>>>
>>>>> thanks.
>>>>> --
>>>>> View this message in context:
>>>>>
>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>> ________________________________
>>>> View message @
>>>>
>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>>>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>>>
>>> ________________________________
>>> View this message in context: Re: the problem to show my ChIP-seq data
>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
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>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>
>>
>>
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: the problem to show my ChIP-seq data

Scott Cain
In reply to this post by Scott Cain
Neil,

Please subscribe to and keep your responses on the GBrowse mailing list.

There is not a tutorial for your specific problem.  If you already
have GFF3, there is some discussion of importing GFF3 into a mysql
database in the tutorial that was installed with gbrowse2:

  http://localhost/gbrowse2/tutorial/tutorial.html#mysql

That tutorial also covers quite a bit about track configuration in
general, and so would probably be helpful to you.  Using the summary
mode is described in this section of the GBrowse2 wiki page:

  http://gmod.org/wiki/GBrowse_2.0_HOWTO#Summary_Mode_.28new_in_version_2.09.29

Scott


On Tue, Jul 27, 2010 at 2:36 PM, neil niu <[hidden email]> wrote:

> Hi Scott,
>
> Exactly, I just want to show a coverage histogram for my blast result.
> But it seems there is no tutorial for my problem and I also know how to
> convert blast result to GFF3.
> but next, I don't know how to import into the GFF3 file and set the track to
> show my summary information.
> I just can study the GB2 tutorial step by step.
> where can I get the tutorial for my problem?
>
> thanks.
>
> On Tue, Jul 27, 2010 at 11:24 AM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Neil,
>>
>> So you would like to create a coverage histogram for your blast
>> results?  Probably the easiest thing to do would be to convert your
>> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
>> import that into a Bio::DB::SeqFeature::Store database, and set the
>> track to show summary information.  That would save you the trouble of
>> calculating the coverage yourself.  Of course, there are multiple
>> steps in those few sentences, so I'll let you get started on that and
>> you can come back here or go to the BioPerl mail list as appropriate
>> for more detailed questions.
>>
>> Scott
>>
>>
>> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>> > Hi Adam,
>> >
>> > Thanks.
>> > I just want to get the reads coverage of genome from BLAST results and
>> > show
>> > like this png graph. it is not ChIP-seq data just 454 reads aligned to
>> > reference genome.
>> > http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>> >
>> > I don't have to get subtracks and I just want to get one track like this
>> > png
>> > is ok.
>> > but I don't know how to set config file and GFF file format for this
>> > png .
>> >
>> > thanks again.
>> >
>> >
>> >
>> >
>> > On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism
>> > System Database] <[hidden email]> wrote:
>> >>
>> >> Hi Neil,
>> >>
>> >> does this give you what you want?
>> >>
>> >>
>> >>
>> >> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>> >>
>> >> You will probably have to upload your data using something like this
>> >> approach:
>> >>
>> >> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>> >>
>> >> adam
>> >>
>> >>
>> >> On 26 Jul 2010, at 20:05, neil wrote:
>> >>
>> >> >
>> >> > I want to show my reads to reference genome alignment result like
>> >> > these:
>> >> > http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>> >> > (the modENCODE tracks example)
>> >> >
>> >> > are there any example config file and GFF file like volvox tutorial
>> >> > example?
>> >> > so, I can show my dataset follw the exmple.
>> >> >
>> >> > thanks.
>> >> > --
>> >> > View this message in context:
>> >> >
>> >> > http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>> >> > Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > 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://ad.doubleclick.net/clk;226879339;13503038;l?
>> >> > http://clk.atdmt.com/CRS/go/247765532/direct/01/
>> >> > _______________________________________________
>> >> > Gmod-gbrowse mailing list
>> >> > [hidden email]
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>> >> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>> >> _______________________________________________
>> >> Gmod-gbrowse mailing list
>> >> [hidden email]
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>
>> >>
>> >> ________________________________
>> >> View message @
>> >>
>> >> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>> >> To unsubscribe from the problem to show my ChIP-seq data, click here.
>> >
>> >
>> > ________________________________
>> > View this message in context: Re: the problem to show my ChIP-seq data
>> > Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > 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://ad.doubleclick.net/clk;226879339;13503038;l?
>> > http://clk.atdmt.com/CRS/go/247765532/direct/01/
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > 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
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: the problem to show my ChIP-seq data

J.M.P. Alves
In reply to this post by Scott Cain
Thanks a lot, Scott. Now it works (there was no mention to "blasttable"
in the script's help...), apparently.

J

Scott Cain wrote:

> Hi J,
>
> I'm not the author of that tool, but my recollection is that it
> supports any format that Bio::SearchIO supports:
>
>          blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)
>          fasta      FASTA ‐m9 and ‐m0
>          blasttable BLAST ‐m9 or ‐m8 output (both NCBI and WUBLAST tabular)
>          megablast  MEGABLAST
>          psl        UCSC PSL format
>          waba       WABA output
>          axt        AXT format
>          sim4       Sim4
>          hmmer      HMMER hmmpfam and hmmsearch
>          exonerate  Exonerate CIGAR and VULGAR format
>          blastxml   NCBI BLAST XML
>          wise       Genewise ‐genesf format
>
> You have to set the format with a command line flag, eg: -f
> blasttable; the default is blast.
>
> Scott
>
>
> On Tue, Jul 27, 2010 at 2:56 PM, J.M.P. Alves <[hidden email]> wrote:
>> Hi, Scott
>>
>> Does bp_search2gff.pl accept tabular BLAST results? The documentation is
>> very sparse on this, but I have tried that and got an empty file:
>>
>> zcat blastres2_Bc_NO_endo_contigs.fas.gz | bp_search2gff.pl -s TBLASTN -o
>> BCU_tblastn.gff3 --version 3
>>
>> Thanks
>> J
>>
>> Scott Cain wrote:
>>> Hi Neil,
>>>
>>> So you would like to create a coverage histogram for your blast
>>> results?  Probably the easiest thing to do would be to convert your
>>> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
>>> import that into a Bio::DB::SeqFeature::Store database, and set the
>>> track to show summary information.  That would save you the trouble of
>>> calculating the coverage yourself.  Of course, there are multiple
>>> steps in those few sentences, so I'll let you get started on that and
>>> you can come back here or go to the BioPerl mail list as appropriate
>>> for more detailed questions.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>>>> Hi Adam,
>>>>
>>>> Thanks.
>>>> I just want to get the reads coverage of genome from BLAST results and
>>>> show
>>>> like this png graph. it is not ChIP-seq data just 454 reads aligned to
>>>> reference genome.
>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>
>>>> I don't have to get subtracks and I just want to get one track like this
>>>> png
>>>> is ok.
>>>> but I don't know how to set config file and GFF file format for this png
>>>> .
>>>>
>>>> thanks again.
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism
>>>> System Database] <[hidden email]> wrote:
>>>>> Hi Neil,
>>>>>
>>>>> does this give you what you want?
>>>>>
>>>>>
>>>>>
>>>>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>>>>
>>>>> You will probably have to upload your data using something like this
>>>>> approach:
>>>>>
>>>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>>>
>>>>> adam
>>>>>
>>>>>
>>>>> On 26 Jul 2010, at 20:05, neil wrote:
>>>>>
>>>>>> I want to show my reads to reference genome alignment result like
>>>>>> these:
>>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>>> (the modENCODE tracks example)
>>>>>>
>>>>>> are there any example config file and GFF file like volvox tutorial
>>>>>> example?
>>>>>> so, I can show my dataset follw the exmple.
>>>>>>
>>>>>> thanks.
>>>>>> --
>>>>>> View this message in context:
>>>>>>
>>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>> ________________________________
>>>>> View message @
>>>>>
>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>>>>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>>>> ________________________________
>>>> View this message in context: Re: the problem to show my ChIP-seq data
>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>
>>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>
>
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


------------------------------------------------------------------------------
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of $1 Million in cash or HP Products. Visit us here for more details:
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Re: the problem to show my ChIP-seq data

J.M.P. Alves
In reply to this post by Scott Cain
OK, the GFF3 file for the BLAST results got generated, and I tried to
load it to a GBrowse 2 instance. The loading looks fine, but when I try
to view it I don't see anything in the track. It used to work without
trouble in GBrowse 1.x and GFF2, which was what I adapted to do this.
Any tutorial out there on loading and showing BLAST results in GBrowse 2
and using GFF3?

The loading was done with:

bp_seqfeature_load.pl -c -d BCU_gb  BCU_headers.gff3
asgard_dna_NO_endo/BCU_tblastn.gff3 Bc_contigs.fas

There were no errors nor warnings. The very end of the loading process:

282000 features loaded in 961.28s ( 3.42s/1000 features)...
                                           283000 features loaded in
964.74s ( 3.47s/1000 features)...
                 284000 features loaded in 968.19s ( 3.44s/1000
features)...
285000 features loaded in 971.63s ( 3.44s/1000 features)...
                                           Building object tree...
0.00s.30s

load time: 989.46s
loading Bc_NO_endo_contigs.fas...
Building object tree... 0.00s

load time: 998.87s

Here are the first few lines of the GFF3 with the BLAST results:

##gff-version 3
BCU_c04258 TBLASTN similarity 26332 27588 589 + 0
Target=Sequence:UniRef100_Q25223 1
  422;score=589
BCU_c01058 TBLASTN similarity 7294 7524 80.1 - 0
Target=Sequence:UniRef100_Q25223 2
33 309;score=80.1
BCU_c01058 TBLASTN similarity 8116 8283 80.1 - 0
Target=Sequence:UniRef100_Q25223 1
  56;score=80.1

My contigs are the BCU_* ones. This was TBLASTN of uniprot sequences
against the contigs.

The BCU_headers.gff3 file has the sequence-region lines, like:

##gff-version 3
##sequence-region BCU_c00249 1 266618
##sequence-region BCU_c00113 1 195546
##sequence-region BCU_c03041 1 147224
##sequence-region BCU_c03169c 1 145712
##sequence-region BCU_c01565 1 71469
##sequence-region BCU_c00250 1 68639
##sequence-region BCU_c03982 1 61104
##sequence-region BCU_c04258 1 59392
##sequence-region BCU_c00243 1 54649
etc.

The track definition stanza looks like:

[TBLASTN]
feature      = TBLASTN
bgcolor      = sub {
                 my $feature = shift;
                 my $strand    = $feature->strand;
                 if ($strand == -1) {
                    return 'red';
                 } else {
                    return 'blue';
                 }
         }
glyph        = graded_segments
min_score    = 1
max_score    = 5000
description  = 1
stranded     = 1
bump_density = 100
label_density= 100
link         = http://www.uniprot.org/uniprot/$name
title        = Search Uniprot for $name
link_target  = _blank
key          = TBLASTN alignments
citation     = TBLASTN matches at E-value 1E-6 or better

Thanks for any pointers.
Cheers

J

Scott Cain wrote:

> Hi J,
>
> I'm not the author of that tool, but my recollection is that it
> supports any format that Bio::SearchIO supports:
>
>          blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)
>          fasta      FASTA ‐m9 and ‐m0
>          blasttable BLAST ‐m9 or ‐m8 output (both NCBI and WUBLAST tabular)
>          megablast  MEGABLAST
>          psl        UCSC PSL format
>          waba       WABA output
>          axt        AXT format
>          sim4       Sim4
>          hmmer      HMMER hmmpfam and hmmsearch
>          exonerate  Exonerate CIGAR and VULGAR format
>          blastxml   NCBI BLAST XML
>          wise       Genewise ‐genesf format
>
> You have to set the format with a command line flag, eg: -f
> blasttable; the default is blast.
>
> Scott
>
>
> On Tue, Jul 27, 2010 at 2:56 PM, J.M.P. Alves <[hidden email]> wrote:
>> Hi, Scott
>>
>> Does bp_search2gff.pl accept tabular BLAST results? The documentation is
>> very sparse on this, but I have tried that and got an empty file:
>>
>> zcat blastres2_Bc_NO_endo_contigs.fas.gz | bp_search2gff.pl -s TBLASTN -o
>> BCU_tblastn.gff3 --version 3
>>
>> Thanks
>> J
>>
>> Scott Cain wrote:
>>> Hi Neil,
>>>
>>> So you would like to create a coverage histogram for your blast
>>> results?  Probably the easiest thing to do would be to convert your
>>> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
>>> import that into a Bio::DB::SeqFeature::Store database, and set the
>>> track to show summary information.  That would save you the trouble of
>>> calculating the coverage yourself.  Of course, there are multiple
>>> steps in those few sentences, so I'll let you get started on that and
>>> you can come back here or go to the BioPerl mail list as appropriate
>>> for more detailed questions.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>>>> Hi Adam,
>>>>
>>>> Thanks.
>>>> I just want to get the reads coverage of genome from BLAST results and
>>>> show
>>>> like this png graph. it is not ChIP-seq data just 454 reads aligned to
>>>> reference genome.
>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>
>>>> I don't have to get subtracks and I just want to get one track like this
>>>> png
>>>> is ok.
>>>> but I don't know how to set config file and GFF file format for this png
>>>> .
>>>>
>>>> thanks again.
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model Organism
>>>> System Database] <[hidden email]> wrote:
>>>>> Hi Neil,
>>>>>
>>>>> does this give you what you want?
>>>>>
>>>>>
>>>>>
>>>>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>>>>
>>>>> You will probably have to upload your data using something like this
>>>>> approach:
>>>>>
>>>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>>>
>>>>> adam
>>>>>
>>>>>
>>>>> On 26 Jul 2010, at 20:05, neil wrote:
>>>>>
>>>>>> I want to show my reads to reference genome alignment result like
>>>>>> these:
>>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>>> (the modENCODE tracks example)
>>>>>>
>>>>>> are there any example config file and GFF file like volvox tutorial
>>>>>> example?
>>>>>> so, I can show my dataset follw the exmple.
>>>>>>
>>>>>> thanks.
>>>>>> --
>>>>>> View this message in context:
>>>>>>
>>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>> ________________________________
>>>>> View message @
>>>>>
>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>>>>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>>>> ________________________________
>>>> View this message in context: Re: the problem to show my ChIP-seq data
>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>
>>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>
>
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


------------------------------------------------------------------------------
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://ad.doubleclick.net/clk;226879339;13503038;l?
http://clk.atdmt.com/CRS/go/247765532/direct/01/
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Re: the problem to show my ChIP-seq data

Scott Cain
Hi J,

At the very least, you want "feature=similarity"  or
"feature=similarity:TBLASTN"

Scott

On Tue, Jul 27, 2010 at 4:53 PM, J.M.P. Alves <[hidden email]> wrote:

> OK, the GFF3 file for the BLAST results got generated, and I tried to load
> it to a GBrowse 2 instance. The loading looks fine, but when I try to view
> it I don't see anything in the track. It used to work without trouble in
> GBrowse 1.x and GFF2, which was what I adapted to do this. Any tutorial out
> there on loading and showing BLAST results in GBrowse 2 and using GFF3?
>
> The loading was done with:
>
> bp_seqfeature_load.pl -c -d BCU_gb  BCU_headers.gff3
> asgard_dna_NO_endo/BCU_tblastn.gff3 Bc_contigs.fas
>
> There were no errors nor warnings. The very end of the loading process:
>
> 282000 features loaded in 961.28s ( 3.42s/1000 features)...
>                           283000 features loaded in 964.74s ( 3.47s/1000
> features)...                 284000 features loaded in 968.19s ( 3.44s/1000
> features)... 285000 features loaded in 971.63s ( 3.44s/1000 features)...
>                                       Building object tree... 0.00s.30s
> load time: 989.46s
> loading Bc_NO_endo_contigs.fas...
> Building object tree... 0.00s
> load time: 998.87s
>
> Here are the first few lines of the GFF3 with the BLAST results:
>
> ##gff-version 3
> BCU_c04258      TBLASTN similarity      26332   27588   589     +       0
> Target=Sequence:UniRef100_Q25223 1
>  422;score=589
> BCU_c01058      TBLASTN similarity      7294    7524    80.1    -       0
> Target=Sequence:UniRef100_Q25223 2
> 33 309;score=80.1
> BCU_c01058      TBLASTN similarity      8116    8283    80.1    -       0
> Target=Sequence:UniRef100_Q25223 1
>  56;score=80.1
>
> My contigs are the BCU_* ones. This was TBLASTN of uniprot sequences against
> the contigs.
>
> The BCU_headers.gff3 file has the sequence-region lines, like:
>
> ##gff-version 3
> ##sequence-region BCU_c00249 1 266618
> ##sequence-region BCU_c00113 1 195546
> ##sequence-region BCU_c03041 1 147224
> ##sequence-region BCU_c03169c 1 145712
> ##sequence-region BCU_c01565 1 71469
> ##sequence-region BCU_c00250 1 68639
> ##sequence-region BCU_c03982 1 61104
> ##sequence-region BCU_c04258 1 59392
> ##sequence-region BCU_c00243 1 54649
> etc.
>
> The track definition stanza looks like:
>
> [TBLASTN]
> feature      = TBLASTN
> bgcolor      = sub {
>                my $feature = shift;
>                my $strand    = $feature->strand;
>                if ($strand == -1) {
>                   return 'red';
>                } else {
>                   return 'blue';
>                }
>        }
> glyph        = graded_segments
> min_score    = 1
> max_score    = 5000
> description  = 1
> stranded     = 1
> bump_density = 100
> label_density= 100
> link         = http://www.uniprot.org/uniprot/$name
> title        = Search Uniprot for $name
> link_target  = _blank
> key          = TBLASTN alignments
> citation     = TBLASTN matches at E-value 1E-6 or better
>
> Thanks for any pointers.
> Cheers
>
> J
>
> Scott Cain wrote:
>>
>> Hi J,
>>
>> I'm not the author of that tool, but my recollection is that it
>> supports any format that Bio::SearchIO supports:
>>
>>         blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)
>>         fasta      FASTA ‐m9 and ‐m0
>>         blasttable BLAST ‐m9 or ‐m8 output (both NCBI and WUBLAST tabular)
>>         megablast  MEGABLAST
>>         psl        UCSC PSL format
>>         waba       WABA output
>>         axt        AXT format
>>         sim4       Sim4
>>         hmmer      HMMER hmmpfam and hmmsearch
>>         exonerate  Exonerate CIGAR and VULGAR format
>>         blastxml   NCBI BLAST XML
>>         wise       Genewise ‐genesf format
>>
>> You have to set the format with a command line flag, eg: -f
>> blasttable; the default is blast.
>>
>> Scott
>>
>>
>> On Tue, Jul 27, 2010 at 2:56 PM, J.M.P. Alves <[hidden email]> wrote:
>>>
>>> Hi, Scott
>>>
>>> Does bp_search2gff.pl accept tabular BLAST results? The documentation is
>>> very sparse on this, but I have tried that and got an empty file:
>>>
>>> zcat blastres2_Bc_NO_endo_contigs.fas.gz | bp_search2gff.pl -s TBLASTN -o
>>> BCU_tblastn.gff3 --version 3
>>>
>>> Thanks
>>> J
>>>
>>> Scott Cain wrote:
>>>>
>>>> Hi Neil,
>>>>
>>>> So you would like to create a coverage histogram for your blast
>>>> results?  Probably the easiest thing to do would be to convert your
>>>> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
>>>> import that into a Bio::DB::SeqFeature::Store database, and set the
>>>> track to show summary information.  That would save you the trouble of
>>>> calculating the coverage yourself.  Of course, there are multiple
>>>> steps in those few sentences, so I'll let you get started on that and
>>>> you can come back here or go to the BioPerl mail list as appropriate
>>>> for more detailed questions.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>>>>>
>>>>> Hi Adam,
>>>>>
>>>>> Thanks.
>>>>> I just want to get the reads coverage of genome from BLAST results and
>>>>> show
>>>>> like this png graph. it is not ChIP-seq data just 454 reads aligned to
>>>>> reference genome.
>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>>
>>>>> I don't have to get subtracks and I just want to get one track like
>>>>> this
>>>>> png
>>>>> is ok.
>>>>> but I don't know how to set config file and GFF file format for this
>>>>> png
>>>>> .
>>>>>
>>>>> thanks again.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model
>>>>> Organism
>>>>> System Database] <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Neil,
>>>>>>
>>>>>> does this give you what you want?
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>>>>>
>>>>>> You will probably have to upload your data using something like this
>>>>>> approach:
>>>>>>
>>>>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>>>>
>>>>>> adam
>>>>>>
>>>>>>
>>>>>> On 26 Jul 2010, at 20:05, neil wrote:
>>>>>>
>>>>>>> I want to show my reads to reference genome alignment result like
>>>>>>> these:
>>>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>>>> (the modENCODE tracks example)
>>>>>>>
>>>>>>> are there any example config file and GFF file like volvox tutorial
>>>>>>> example?
>>>>>>> so, I can show my dataset follw the exmple.
>>>>>>>
>>>>>>> thanks.
>>>>>>> --
>>>>>>> View this message in context:
>>>>>>>
>>>>>>>
>>>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>>> _______________________________________________
>>>>>>> Gmod-gbrowse mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>> View message @
>>>>>>
>>>>>>
>>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>>>>>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>>>>>
>>>>> ________________________________
>>>>> View this message in context: Re: the problem to show my ChIP-seq data
>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>
>>>>
>>> --
>>> -------------------------------
>>> João Marcelo Pereira Alves (J)
>>> Post-doctoral fellow
>>> MCV / VCU - Richmond, VA
>>> http://bioinfo.lpb.mic.vcu.edu
>>> f. 1-804-828-3897
>>>
>>>
>>
>>
>>
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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of $1 Million in cash or HP Products. Visit us here for more details:
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Re: the problem to show my ChIP-seq data

J.M.P. Alves
Thanks, Scott.

It worked perfectly after I changed that -- and also removed the
"Sequence:" that is added by bp_search2gff.pl between Target= and the
sequence identifier (that breaks the link out).

J

Scott Cain wrote:

> Hi J,
>
> At the very least, you want "feature=similarity"  or
> "feature=similarity:TBLASTN"
>
> Scott
>
> On Tue, Jul 27, 2010 at 4:53 PM, J.M.P. Alves <[hidden email]> wrote:
>> OK, the GFF3 file for the BLAST results got generated, and I tried to load
>> it to a GBrowse 2 instance. The loading looks fine, but when I try to view
>> it I don't see anything in the track. It used to work without trouble in
>> GBrowse 1.x and GFF2, which was what I adapted to do this. Any tutorial out
>> there on loading and showing BLAST results in GBrowse 2 and using GFF3?
>>
>> The loading was done with:
>>
>> bp_seqfeature_load.pl -c -d BCU_gb  BCU_headers.gff3
>> asgard_dna_NO_endo/BCU_tblastn.gff3 Bc_contigs.fas
>>
>> There were no errors nor warnings. The very end of the loading process:
>>
>> 282000 features loaded in 961.28s ( 3.42s/1000 features)...
>>                           283000 features loaded in 964.74s ( 3.47s/1000
>> features)...                 284000 features loaded in 968.19s ( 3.44s/1000
>> features)... 285000 features loaded in 971.63s ( 3.44s/1000 features)...
>>                                       Building object tree... 0.00s.30s
>> load time: 989.46s
>> loading Bc_NO_endo_contigs.fas...
>> Building object tree... 0.00s
>> load time: 998.87s
>>
>> Here are the first few lines of the GFF3 with the BLAST results:
>>
>> ##gff-version 3
>> BCU_c04258      TBLASTN similarity      26332   27588   589     +       0
>> Target=Sequence:UniRef100_Q25223 1
>>  422;score=589
>> BCU_c01058      TBLASTN similarity      7294    7524    80.1    -       0
>> Target=Sequence:UniRef100_Q25223 2
>> 33 309;score=80.1
>> BCU_c01058      TBLASTN similarity      8116    8283    80.1    -       0
>> Target=Sequence:UniRef100_Q25223 1
>>  56;score=80.1
>>
>> My contigs are the BCU_* ones. This was TBLASTN of uniprot sequences against
>> the contigs.
>>
>> The BCU_headers.gff3 file has the sequence-region lines, like:
>>
>> ##gff-version 3
>> ##sequence-region BCU_c00249 1 266618
>> ##sequence-region BCU_c00113 1 195546
>> ##sequence-region BCU_c03041 1 147224
>> ##sequence-region BCU_c03169c 1 145712
>> ##sequence-region BCU_c01565 1 71469
>> ##sequence-region BCU_c00250 1 68639
>> ##sequence-region BCU_c03982 1 61104
>> ##sequence-region BCU_c04258 1 59392
>> ##sequence-region BCU_c00243 1 54649
>> etc.
>>
>> The track definition stanza looks like:
>>
>> [TBLASTN]
>> feature      = TBLASTN
>> bgcolor      = sub {
>>                my $feature = shift;
>>                my $strand    = $feature->strand;
>>                if ($strand == -1) {
>>                   return 'red';
>>                } else {
>>                   return 'blue';
>>                }
>>        }
>> glyph        = graded_segments
>> min_score    = 1
>> max_score    = 5000
>> description  = 1
>> stranded     = 1
>> bump_density = 100
>> label_density= 100
>> link         = http://www.uniprot.org/uniprot/$name
>> title        = Search Uniprot for $name
>> link_target  = _blank
>> key          = TBLASTN alignments
>> citation     = TBLASTN matches at E-value 1E-6 or better
>>
>> Thanks for any pointers.
>> Cheers
>>
>> J
>>
>> Scott Cain wrote:
>>> Hi J,
>>>
>>> I'm not the author of that tool, but my recollection is that it
>>> supports any format that Bio::SearchIO supports:
>>>
>>>         blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)
>>>         fasta      FASTA ‐m9 and ‐m0
>>>         blasttable BLAST ‐m9 or ‐m8 output (both NCBI and WUBLAST tabular)
>>>         megablast  MEGABLAST
>>>         psl        UCSC PSL format
>>>         waba       WABA output
>>>         axt        AXT format
>>>         sim4       Sim4
>>>         hmmer      HMMER hmmpfam and hmmsearch
>>>         exonerate  Exonerate CIGAR and VULGAR format
>>>         blastxml   NCBI BLAST XML
>>>         wise       Genewise ‐genesf format
>>>
>>> You have to set the format with a command line flag, eg: -f
>>> blasttable; the default is blast.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jul 27, 2010 at 2:56 PM, J.M.P. Alves <[hidden email]> wrote:
>>>> Hi, Scott
>>>>
>>>> Does bp_search2gff.pl accept tabular BLAST results? The documentation is
>>>> very sparse on this, but I have tried that and got an empty file:
>>>>
>>>> zcat blastres2_Bc_NO_endo_contigs.fas.gz | bp_search2gff.pl -s TBLASTN -o
>>>> BCU_tblastn.gff3 --version 3
>>>>
>>>> Thanks
>>>> J
>>>>
>>>> Scott Cain wrote:
>>>>> Hi Neil,
>>>>>
>>>>> So you would like to create a coverage histogram for your blast
>>>>> results?  Probably the easiest thing to do would be to convert your
>>>>> blast results to GFF3 using BioPerl's bp_search2gff.pl script and
>>>>> import that into a Bio::DB::SeqFeature::Store database, and set the
>>>>> track to show summary information.  That would save you the trouble of
>>>>> calculating the coverage yourself.  Of course, there are multiple
>>>>> steps in those few sentences, so I'll let you get started on that and
>>>>> you can come back here or go to the BioPerl mail list as appropriate
>>>>> for more detailed questions.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jul 27, 2010 at 1:49 PM, neil <[hidden email]> wrote:
>>>>>> Hi Adam,
>>>>>>
>>>>>> Thanks.
>>>>>> I just want to get the reads coverage of genome from BLAST results and
>>>>>> show
>>>>>> like this png graph. it is not ChIP-seq data just 454 reads aligned to
>>>>>> reference genome.
>>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>>>
>>>>>> I don't have to get subtracks and I just want to get one track like
>>>>>> this
>>>>>> png
>>>>>> is ok.
>>>>>> but I don't know how to set config file and GFF file format for this
>>>>>> png
>>>>>> .
>>>>>>
>>>>>> thanks again.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Jul 27, 2010 at 2:16 AM, Adam Witney [via Generic Model
>>>>>> Organism
>>>>>> System Database] <[hidden email]> wrote:
>>>>>>> Hi Neil,
>>>>>>>
>>>>>>> does this give you what you want?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2#Multidimensional_Subtracks
>>>>>>>
>>>>>>> You will probably have to upload your data using something like this
>>>>>>> approach:
>>>>>>>
>>>>>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>>>>>
>>>>>>> adam
>>>>>>>
>>>>>>>
>>>>>>> On 26 Jul 2010, at 20:05, neil wrote:
>>>>>>>
>>>>>>>> I want to show my reads to reference genome alignment result like
>>>>>>>> these:
>>>>>>>> http://gmod.org/wiki/Image:Subtrack_selection_table_overview.png
>>>>>>>> (the modENCODE tracks example)
>>>>>>>>
>>>>>>>> are there any example config file and GFF file like volvox tutorial
>>>>>>>> example?
>>>>>>>> so, I can show my dataset follw the exmple.
>>>>>>>>
>>>>>>>> thanks.
>>>>>>>> --
>>>>>>>> View this message in context:
>>>>>>>>
>>>>>>>>
>>>>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2228425.html
>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>>> _______________________________________________
>>>>>>> Gmod-gbrowse mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>
>>>>>>>
>>>>>>> ________________________________
>>>>>>> View message @
>>>>>>>
>>>>>>>
>>>>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/the-problem-to-show-my-ChIP-seq-data-tp2228425p2255581.html
>>>>>>> To unsubscribe from the problem to show my ChIP-seq data, click here.
>>>>>> ________________________________
>>>>>> View this message in context: Re: the problem to show my ChIP-seq data
>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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://ad.doubleclick.net/clk;226879339;13503038;l?
>>>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>>
>>>>>
>>>> --
>>>> -------------------------------
>>>> João Marcelo Pereira Alves (J)
>>>> Post-doctoral fellow
>>>> MCV / VCU - Richmond, VA
>>>> http://bioinfo.lpb.mic.vcu.edu
>>>> f. 1-804-828-3897
>>>>
>>>>
>>>
>>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>
>
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


------------------------------------------------------------------------------
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://ad.doubleclick.net/clk;226879339;13503038;l?
http://clk.atdmt.com/CRS/go/247765532/direct/01/
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