Hi Aman,

For TopHat, the option is named:

"Will you select a reference genome from your history or use a built-in index?:"

set this to be "Use one from the history"

and the form with refresh. The option named:

"Select the reference genome:"

will now contain all history datasets of the appropriate format, rather than a list of native indexed dataset names. This is where you would select your reference genome, that is a fasta format dataset, in your history.

Take care,

Jen Galaxy team

On 1/16/12 7:58 PM, Amandeep Sidhu wrote:

Dear Jennifer,

Top hat does does not have the option of using custom genomes from history like other tools. It says that if reference genome needs to be added contact galaxy team.

Thanks.

Regards, Aman.

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Sent from Aman's iPad @biomap | http://amandeep.org/ | http://biomap.org/

On 17/01/2012, at 10:37, "Jennifer Jackson"jen@bx.psu.edu wrote:

...

Hello Aman,

The quickest way to use new genomes with tools is to use them as a custom reference genome. To do this, load the genome in fasta format into your history and set the tool form option to use the reference genome "from the history".

Best practices: 1 - double check that the format is strict fasta (all lines wrapped to same length, no extra lines or hidden characters, sequence identifiers are unique). 2 - use the same genome dataset for all steps within an analysis 3 - load using FTP and make certain load is complete http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP

Hopefully this helps!

Best,

Jen Galaxy team

On 1/14/12 6:32 PM, Amandeep Sidhu wrote:

...

Hi All,

We need Vicugna Pacos (http://asia.ensembl.org/Vicugna_pacos/Info/Index) added as a reference genome to run analysis using Top Hat on the public server.

Thanks.

Regards, Aman.

---

Sent from Aman's iPad @biomap | http://amandeep.org/ | http://biomap.org/

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