Hi, It doesn't actually matter if they are the same, because unfortunately there is no means of uploading index files to Galaxy. There are other reasons, too, but the different platforms issue is one reason we did not set it up so people could upload index files. Regards, Kelly On Jun 9, 2010, at 2:43 PM, Whyte, Jeffrey wrote:

Hello Kelly,

When I re-read your message, I noticed that you said the index needed to be built on the same platform that Bowtie will be running on.

The swine index that I have was built with Bowtie on a the system listed below. Is this compatible with the platform that Bowtie on Galaxy is running on?

Thanks very much, Jeff

Dell 1850 Dual Core Cluster

$ uname -s -r -v -p -i -o -v Linux 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 GNU/Linux

----- Jeffrey J. Whyte, PhD Department of Biomedical Sciences University of Missouri-Columbia

On Jun 8, 2010, at 2:48 PM, Kelly Vincent wrote:

...

Hello,

Unfortunately, it is not possible for you to upload the actual index files to public Galaxy (the indexes usually need to be built on the same platform that Bowtie will be running on), so the only option when the indexes aren't offered built-in is to supply the fasta. However, as James just mentioned, we can prepare the swine index files ourselves and provide them as a built-in option. It will just take a few days to get in place. Could you let me know where I can get the reference? If it's not from UCSC (our standard source), it might take longer to get it in place.

Thanks, Kelly

On Tue 8 Jun 2010, at 3:42 PM, Whyte, Jeffrey wrote:

...

Thanks so much for the rapid response, Kelly.

Just to clarify, if I already have the genome indexed as .ebwt files and upload these, will Galaxy still take longer? We have Bowtie on our Linux cluster, but I like the unified features of Galaxy. I will let you know if any issues come up.

Greatly resource!

Jeff ----- Jeffrey J. Whyte, PhD Department of Biomedical Sciences University of Missouri-Columbia

On Jun 8, 2010, at 2:26 PM, Kelly Vincent wrote:

...

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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