[Gmod-ajax] VCF data not showing on track

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[Gmod-ajax] VCF data not showing on track

Venice Margarette Juanillas-2
Hi Robert,

I have successfully installed JBrowse on a VM machine. I could view the Reference Sequence and some sample VCF file that I downloaded from the 1000 Genomes. But when I tried to add our custom vcf data, it just doesn't display. I attached a screenshot of how my data/tracks.conf look like. Any suggestions on what I should do?

Inline image 3

Also, I noted that the data that were displayed were those which have vcf format version 4.0, while all our custom data are in version 4.1. So I have to ask, does it have to do with the vcf version?

Thanks and Best Regards,
Venice



--
Venice Margarette B. Juanillas
TTC-Genetic Resources Center
Email: [hidden email]

Genotyping Services Laboratory<img width="16" height="16" src="data:image/gif;base64,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">
Plant Breeding, Genetics and Biotechnology Division
International Rice Research Institute
DAPO Box 7777, Metro Manila
PHILIPPINES
Tel: +63(49) 536-2701 ext 2678
Website: gsl.irri.org



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Re: VCF data not showing on track

Robert Buels-2
Very often, when people write emails like this to the list, it turns out
to be caused by the names of the chromosomes being different in
different parts of their data.  JBrowse does a bit of "regularization"
of chromosome names behind the scenes to try to smooth this over
somewhat but can't fix everything.

In particular, if your VCF file has chromosomes named like "1", "2", etc
and the reference sequences you formatted are named like "Chr1", "Chr2",
etc, JBrowse won't know that these are the same.

Check the reference sequence names in your TR22183.* vcf files.  Is that
the problem?

Rob


On 03/06/2014 07:54 PM, Venice Margarette Juanillas wrote:

> Hi Robert,
>
> I have successfully installed JBrowse on a VM machine. I could view the
> Reference Sequence and some sample VCF file that I downloaded from the
> 1000 Genomes. But when I tried to add our custom vcf data, it just
> doesn't display. I attached a screenshot of how my data/tracks.conf look
> like. Any suggestions on what I should do?
>
> Inline image 3
>
> Also, I noted that the data that were displayed were those which have
> vcf format version 4.0, while all our custom data are in version 4.1. So
> I have to ask, does it have to do with the vcf version?
>
> Thanks and Best Regards,
> Venice
>
>
>
> --
> *_Venice Margarette B. Juanillas_*
> *TTC-Genetic Resources Center*
> Email: [hidden email] <mailto:[hidden email]>
> Tel: +63(49) 536-2701 ext 2324
>
> *Genotyping Services Laboratory*
> Plant Breeding, Genetics and Biotechnology Division
> International Rice Research Institute
> DAPO Box 7777, Metro Manila
> PHILIPPINES
> Tel: +63(49) 536-2701 ext 2678
> Website: gsl.irri.org <http://gsl.irri.org/>
>
> *
> *

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With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
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Re: VCF data not showing on track

Venice Margarette Juanillas-2
Hi Robert,

No the sequence names are similarly formatted. They are named as "chr01|msu7,chr02|msu7,chr03|msu7,..."

Thank you very much.

Cheers,
 Venice


On Sun, Mar 9, 2014 at 11:57 PM, Robert Buels <[hidden email]> wrote:
Very often, when people write emails like this to the list, it turns out to be caused by the names of the chromosomes being different in different parts of their data.  JBrowse does a bit of "regularization" of chromosome names behind the scenes to try to smooth this over somewhat but can't fix everything.

In particular, if your VCF file has chromosomes named like "1", "2", etc and the reference sequences you formatted are named like "Chr1", "Chr2", etc, JBrowse won't know that these are the same.

Check the reference sequence names in your TR22183.* vcf files.  Is that the problem?

Rob



On 03/06/2014 07:54 PM, Venice Margarette Juanillas wrote:
Hi Robert,

I have successfully installed JBrowse on a VM machine. I could view the
Reference Sequence and some sample VCF file that I downloaded from the
1000 Genomes. But when I tried to add our custom vcf data, it just
doesn't display. I attached a screenshot of how my data/tracks.conf look
like. Any suggestions on what I should do?

Inline image 3

Also, I noted that the data that were displayed were those which have
vcf format version 4.0, while all our custom data are in version 4.1. So
I have to ask, does it have to do with the vcf version?

Thanks and Best Regards,
Venice



--
*_Venice Margarette B. Juanillas_*
*TTC-Genetic Resources Center*
Email: [hidden email] <mailto:[hidden email]>

Tel: <a href="tel:%2B63%2849%29%20536-2701%20ext%202324" value="+63495362701" target="_blank">+63(49) 536-2701 ext 2324

*Genotyping Services Laboratory*

Plant Breeding, Genetics and Biotechnology Division
International Rice Research Institute
DAPO Box 7777, Metro Manila
PHILIPPINES
Tel: <a href="tel:%2B63%2849%29%20536-2701%20ext%202678" value="+63495362701" target="_blank">+63(49) 536-2701 ext 2678
Website: gsl.irri.org <http://gsl.irri.org/>

*
*



--
Venice Margarette B. Juanillas
TTC-Genetic Resources Center
Email: [hidden email]

Genotyping Services Laboratory
Plant Breeding, Genetics and Biotechnology Division
International Rice Research Institute
DAPO Box 7777, Metro Manila
PHILIPPINES
Tel: +63(49) 536-2701 ext 2678
Website: gsl.irri.org



------------------------------------------------------------------------------
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applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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Re: VCF data not showing on track

Colin
Those chromosome names are similar but not the same (Chr1 vs chr01). I think it's best to make sure that they are exactly the same.

Thanks,
-Colin


On Sun, Mar 9, 2014 at 8:09 PM, Venice Margarette Juanillas <[hidden email]> wrote:
Hi Robert,

No the sequence names are similarly formatted. They are named as "chr01|msu7,chr02|msu7,chr03|msu7,..."

Thank you very much.

Cheers,
 Venice


On Sun, Mar 9, 2014 at 11:57 PM, Robert Buels <[hidden email]> wrote:
Very often, when people write emails like this to the list, it turns out to be caused by the names of the chromosomes being different in different parts of their data.  JBrowse does a bit of "regularization" of chromosome names behind the scenes to try to smooth this over somewhat but can't fix everything.

In particular, if your VCF file has chromosomes named like "1", "2", etc and the reference sequences you formatted are named like "Chr1", "Chr2", etc, JBrowse won't know that these are the same.

Check the reference sequence names in your TR22183.* vcf files.  Is that the problem?

Rob



On 03/06/2014 07:54 PM, Venice Margarette Juanillas wrote:
Hi Robert,

I have successfully installed JBrowse on a VM machine. I could view the
Reference Sequence and some sample VCF file that I downloaded from the
1000 Genomes. But when I tried to add our custom vcf data, it just
doesn't display. I attached a screenshot of how my data/tracks.conf look
like. Any suggestions on what I should do?

Inline image 3

Also, I noted that the data that were displayed were those which have
vcf format version 4.0, while all our custom data are in version 4.1. So
I have to ask, does it have to do with the vcf version?

Thanks and Best Regards,
Venice



--
*_Venice Margarette B. Juanillas_*
*TTC-Genetic Resources Center*
Email: [hidden email] <mailto:[hidden email]>

Tel: <a href="tel:%2B63%2849%29%20536-2701%20ext%202324" value="+63495362701" target="_blank">+63(49) 536-2701 ext 2324

*Genotyping Services Laboratory*

Plant Breeding, Genetics and Biotechnology Division
International Rice Research Institute
DAPO Box 7777, Metro Manila
PHILIPPINES
Tel: <a href="tel:%2B63%2849%29%20536-2701%20ext%202678" value="+63495362701" target="_blank">+63(49) 536-2701 ext 2678
Website: gsl.irri.org <http://gsl.irri.org/>

*
*



--
Venice Margarette B. Juanillas
TTC-Genetic Resources Center
Email: [hidden email]
Genotyping Services Laboratory
Plant Breeding, Genetics and Biotechnology Division
International Rice Research Institute
DAPO Box 7777, Metro Manila
PHILIPPINES
Tel: +63(49) 536-2701 ext 2678
Website: gsl.irri.org



------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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Re: VCF data not showing on track

Robert Buels-2
Yes, "chr01|msu7" is not at all the same as "Chr1".


On 03/10/2014 11:09 AM, Colin wrote:

> Those chromosome names are similar but not the same (Chr1 vs chr01). I
> think it's best to make sure that they are exactly the same.
>
> Thanks,
> -Colin
>
>
> On Sun, Mar 9, 2014 at 8:09 PM, Venice Margarette Juanillas
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Hi Robert,
>
>     No the sequence names are similarly formatted. They are named as
>     "*chr01|msu7,chr02|msu7,chr03|msu7,...*"
>
>     Thank you very much.
>
>     Cheers,
>       Venice
>
>
>     On Sun, Mar 9, 2014 at 11:57 PM, Robert Buels <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Very often, when people write emails like this to the list, it
>         turns out to be caused by the names of the chromosomes being
>         different in different parts of their data.  JBrowse does a bit
>         of "regularization" of chromosome names behind the scenes to try
>         to smooth this over somewhat but can't fix everything.
>
>         In particular, if your VCF file has chromosomes named like "1",
>         "2", etc and the reference sequences you formatted are named
>         like "Chr1", "Chr2", etc, JBrowse won't know that these are the
>         same.
>
>         Check the reference sequence names in your TR22183.* vcf files.
>           Is that the problem?
>
>         Rob
>
>
>
>         On 03/06/2014 07:54 PM, Venice Margarette Juanillas wrote:
>
>             Hi Robert,
>
>             I have successfully installed JBrowse on a VM machine. I
>             could view the
>             Reference Sequence and some sample VCF file that I
>             downloaded from the
>             1000 Genomes. But when I tried to add our custom vcf data,
>             it just
>             doesn't display. I attached a screenshot of how my
>             data/tracks.conf look
>             like. Any suggestions on what I should do?
>
>             Inline image 3
>
>             Also, I noted that the data that were displayed were those
>             which have
>             vcf format version 4.0, while all our custom data are in
>             version 4.1. So
>             I have to ask, does it have to do with the vcf version?
>
>             Thanks and Best Regards,
>             Venice
>
>
>
>             --
>             *_Venice Margarette B. Juanillas_*
>             *TTC-Genetic Resources Center*
>             Email: [hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>
>
>             Tel: +63(49) 536-2701 ext 2324
>             <tel:%2B63%2849%29%20536-2701%20ext%202324>
>
>             *Genotyping Services Laboratory*
>
>             Plant Breeding, Genetics and Biotechnology Division
>             International Rice Research Institute
>             DAPO Box 7777, Metro Manila
>             PHILIPPINES
>             Tel: +63(49) 536-2701 ext 2678
>             <tel:%2B63%2849%29%20536-2701%20ext%202678>
>             Website: gsl.irri.org <http://gsl.irri.org>
>             <http://gsl.irri.org/>
>
>             *
>             *
>
>
>
>
>     --
>     *_Venice Margarette B. Juanillas_*
>     *TTC-Genetic Resources Center*
>     Email: [hidden email] <mailto:[hidden email]>
>     Tel: +63(49) 536-2701 ext 2324
>
>     *Genotyping Services Laboratory*
>     Plant Breeding, Genetics and Biotechnology Division
>     International Rice Research Institute
>     DAPO Box 7777, Metro Manila
>     PHILIPPINES
>     Tel: +63(49) 536-2701 ext 2678
>     Website: gsl.irri.org <http://gsl.irri.org/>
>
>     *
>     *
>
>     ------------------------------------------------------------------------------
>     Learn Graph Databases - Download FREE O'Reilly Book
>     "Graph Databases" is the definitive new guide to graph databases and
>     their
>     applications. Written by three acclaimed leaders in the field,
>     this first edition is now available. Download your free book today!
>     http://p.sf.net/sfu/13534_NeoTech
>     _______________________________________________
>     Gmod-ajax mailing list
>     [hidden email] <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

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"Graph Databases" is the definitive new guide to graph databases and their
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this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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