On the tool form for "Extract Genomic DNA" a custom genome can be used once the genome is loaded into your history as a fasta file. Instructions for how to load/prepare a custom genome, including a prep screencast and troubleshooting tips, are in this wiki: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes
Once your custom genome is prepped and ready to use, on the tool form for the option "Source for Genomic Data:" choose "History". Another option will refresh on the form named "Using reference file:" where you can select the custom fasta reference genome dataset from your history from a pull down menu of all the fasta files in your history.
Just so you know, a "built-in index" in Galaxy means a reference genome that is native to the instance you are working with (already incorporated, not a custom genome). When using the "Extract" tool, this is interpreted from the assigned database of the input dataset when the option "Locally cached" is used. This can get slightly confusing as not all genomes that can be assigned as a database (on the Edit Attributes form - found by clicking on the pencil icon) are appropriate or available as native indexes for all tools, including the "Extract" tool. The good news is that for the majority of tools where a reference genome is appropriate, a custom genome can be used if your genome is not native. The tool form options vary slightly but the example above for this tool is a good model. Please let us know if you need help with any others.
Good luck with your project!
Jen Galaxy team
On 9/5/12 11:04 AM, Deepthi Theresa wrote:
I want to fetch sequences from a file(in interval format) using custom genome build(using built-in index).
How can I do that?
I tried "fetch sequences" in the menu. But I could not find option for a custom genome.
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