Hello Deeps,
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:
Hi all,
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.
Thanks,
Deeps
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Jennifer Jackson
http://galaxyproject.org
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