Displaying Sequence in Gbrowse Syn

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Displaying Sequence in Gbrowse Syn

Jody Phelan
Hi all,

I have installed GBrowse_syn using mysql databases (human and mouse comparison). I would like to show the nucleotide sequence. It works fine when I am loading the fasta file from the database directory, but when I load the sequence into a mysql database it doesnt seem to load into the browser. I have used the bp_load_gff script on the fasta file downloaded from ucsc. Are there any additional steps required that I have missed?

Regards,
Jody Phelan

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Fwd: Displaying Sequence in Gbrowse Syn

girlwithglasses
Can anyone help Jody with her GBrowse syn question?

---------- Forwarded message ----------
From: Jody Phelan <[hidden email]>
Date: Wed, Dec 5, 2012 at 7:52 AM
Subject: [Gmod-gbrowse] Displaying Sequence in Gbrowse Syn
To: [hidden email]


Hi all,

I have installed GBrowse_syn using mysql databases (human and mouse comparison). I would like to show the nucleotide sequence. It works fine when I am loading the fasta file from the database directory, but when I load the sequence into a mysql database it doesnt seem to load into the browser. I have used the bp_load_gff script on the fasta file downloaded from ucsc. Are there any additional steps required that I have missed?

Regards,
Jody Phelan

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Re: Displaying Sequence in Gbrowse Syn

Scott Cain
In reply to this post by Jody Phelan
Hi Jody,

Nothing obvious.  IS there anything useful in the apache error log?
If you create a simple GBrowse (not gbrowse_syn) config to use your
human or mouse data, does the sequence data show up then?  I ask
because it is generally easier to debug this sort of thing in GBrowse
and then move to GBrowse_syn after the details are working.

Scott


On Wed, Dec 5, 2012 at 10:52 AM, Jody Phelan <[hidden email]> wrote:

> Hi all,
>
> I have installed GBrowse_syn using mysql databases (human and mouse
> comparison). I would like to show the nucleotide sequence. It works fine
> when I am loading the fasta file from the database directory, but when I
> load the sequence into a mysql database it doesnt seem to load into the
> browser. I have used the bp_load_gff script on the fasta file downloaded
> from ucsc. Are there any additional steps required that I have missed?
>
> Regards,
> Jody Phelan
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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