[Gmod-ajax] Renaming reference sequences

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[Gmod-ajax] Renaming reference sequences

pparsons
Hello,

I am new to JBrowse and to genomics in general, so please excuse my ignorance. I do research in the area of interactive visualization and decision support, and have recently started a project that applies this research to the cytogenetics domain.

I have installed JBrowse on a linux server, and everything seems to be working fine. I have also downloaded the GRCh37 reference assembly with the latest patch (p13) to my server and loaded them into JBrowse using prepare-refseqs.pl with the fasta files for each chromosome. All of this worked without problems.

The question I have now is about renaming the reference sequences as they are shown in JBrowse. As it stands now, they are named as such: "gi|224384745|gb|CM000686.1|" but I would rather have it say "chromosome 20" or something more understandable for the user.

Is there a standard way to do this? It seems if I change the names in the json files the sequences are not displayed correctly anymore.

Please advise if you have any thoughts about this issue or any general comments or suggestions.

Thanks,
Paul Parsons

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Re: Renaming reference sequences

Robert Buels-2
It's probably easiest to change the names in your source data file
before you format it with prepare-refseqs.pl.

Changing the names of sequences on the ">" lines of a FASTA file is a
lot easier than editing JSON or having JBrowse change sequence names on
the fly.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/06/2013 02:41 PM, Paul Parsons wrote:

> Hello,
>
> I am new to JBrowse and to genomics in general, so please excuse my
> ignorance. I do research in the area of interactive visualization and
> decision support, and have recently started a project that applies this
> research to the cytogenetics domain.
>
> I have installed JBrowse on a linux server, and everything seems to be
> working fine. I have also downloaded the GRCh37 reference assembly with
> the latest patch (p13) to my server and loaded them into JBrowse using
> prepare-refseqs.pl <http://prepare-refseqs.pl> with the fasta files for
> each chromosome. All of this worked without problems.
>
> The question I have now is about renaming the reference sequences as
> they are shown in JBrowse. As it stands now, they are named as such:
> "gi|224384745|gb|CM000686.1|" but I would rather have it say "chromosome
> 20" or something more understandable for the user.
>
> Is there a standard way to do this? It seems if I change the names in
> the json files the sequences are not displayed correctly anymore.
>
> Please advise if you have any thoughts about this issue or any general
> comments or suggestions.
>
> Thanks,
> Paul Parsons
> www.csd.uwo.ca/~pparsons <http://www.csd.uwo.ca/~pparsons>
>
>
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> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: Renaming reference sequences

pparsons
Excellent, thanks for the quick response!


On Wed, Nov 6, 2013 at 2:54 PM, Robert Buels <[hidden email]> wrote:
It's probably easiest to change the names in your source data file before you format it with prepare-refseqs.pl.

Changing the names of sequences on the ">" lines of a FASTA file is a lot easier than editing JSON or having JBrowse change sequence names on the fly.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org


On 11/06/2013 02:41 PM, Paul Parsons wrote:
Hello,

I am new to JBrowse and to genomics in general, so please excuse my
ignorance. I do research in the area of interactive visualization and
decision support, and have recently started a project that applies this
research to the cytogenetics domain.

I have installed JBrowse on a linux server, and everything seems to be
working fine. I have also downloaded the GRCh37 reference assembly with
the latest patch (p13) to my server and loaded them into JBrowse using
prepare-refseqs.pl <http://prepare-refseqs.pl> with the fasta files for

each chromosome. All of this worked without problems.

The question I have now is about renaming the reference sequences as
they are shown in JBrowse. As it stands now, they are named as such:
"gi|224384745|gb|CM000686.1|" but I would rather have it say "chromosome
20" or something more understandable for the user.

Is there a standard way to do this? It seems if I change the names in
the json files the sequences are not displayed correctly anymore.

Please advise if you have any thoughts about this issue or any general
comments or suggestions.

Thanks,
Paul Parsons
www.csd.uwo.ca/~pparsons <http://www.csd.uwo.ca/~pparsons>


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from the latest Intel processors and coprocessors. See abstracts and register
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