Upload genome index to Galaxy for Bowtie alignment?
Hello, On the Galaxy web interface, the option to map sequences with Bowtie for Illumina reads is listed under the Tools heading "NGS: Mapping". At the top of the page, it states, "Will you select a reference genome from your history or use a built-in index?" The options are: "Use a built-in index" or "Use one from the history". I have a genome index (swine) 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 in advance, Jeff ----- Jeffrey J. Whyte, PhD Department of Biomedical Sciences University of Missouri-Columbia
Jeff, Yes, you can upload your swine reference. Any reference file (in fasta format) can be uploaded through Get Data. Just be aware that using a reference from your history will make Bowtie take longer than with a built-in index every time you map reads (because it has to do the indexing of that file before doing the actual mapping). Let us know if you have any issues. Regards, Kelly On Tue 8 Jun 2010, at 3:19 PM, Whyte, Jeffrey wrote:
Hello,
On the Galaxy web interface, the option to map sequences with Bowtie for Illumina reads is listed under the Tools heading "NGS: Mapping".
At the top of the page, it states, "Will you select a reference genome from your history or use a built-in index?" The options are: "Use a built-in index" or "Use one from the history".
I have a genome index (swine) 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 in advance, Jeff ----- Jeffrey J. Whyte, PhD Department of Biomedical Sciences University of Missouri-Columbia
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Jeffrey, is this a publicly available genome build (e.g. In genbank?). It may be easier to provide the index. -- jt (composed on my phone) On Jun 8, 2010, at 12:19 PM, "Whyte, Jeffrey" <whytej@missouri.edu> wrote:
Hello,
On the Galaxy web interface, the option to map sequences with Bowtie for Illumina reads is listed under the Tools heading "NGS: Mapping".
At the top of the page, it states, "Will you select a reference genome from your history or use a built-in index?" The options are: "Use a built-in index" or "Use one from the history".
I have a genome index (swine) 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 in advance, Jeff ----- Jeffrey J. Whyte, PhD Department of Biomedical Sciences University of Missouri-Columbia
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participants (3)
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James Taylor -
Kelly Vincent -
Whyte, Jeffrey