Upload genome index to Galaxy for Bowtie alignment?

jjw14 · 06-08-2010, 09:22 AM

On the Galaxy web interface, the option to map sequences with Bowtie for Illumina reads is listed under the Tools heading "NGS: Mapping".

"Will you select a reference genome from your history or use a built-in index?" is the first question at the top of the web page. The options are: "Use a built-in index" or "Use one from the history".

If I have a genome index that is not available on the "built-in" list, can I upload this index file to Galaxy under the Get Data page and then select it under "Use one from the history"?

The index file is 3 GB, so any advice is appreciated before I try to upload it.

Thanks,
jjw

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06-08-2010, 09:22 AM	#1
jjw14 Member Location: Missouri Join Date: Apr 2010 Posts: 39	Upload genome index to Galaxy for Bowtie alignment? On the Galaxy web interface, the option to map sequences with Bowtie for Illumina reads is listed under the Tools heading "NGS: Mapping". "Will you select a reference genome from your history or use a built-in index?" is the first question at the top of the web page. The options are: "Use a built-in index" or "Use one from the history". If I have a genome index that is not available on the "built-in" list, can I upload this index file to Galaxy under the Get Data page and then select it under "Use one from the history"? The index file is 3 GB, so any advice is appreciated before I try to upload it. Thanks, jjw