Upload genome index to Galaxy for Bowtie alignment?

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Upload genome index to Galaxy for Bowtie alignment?

jjw14
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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Re: Upload genome index to Galaxy for Bowtie alignment?

Kelly Vincent-2
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
>
>
> _______________________________________________
> galaxy-user mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: Upload genome index to Galaxy for Bowtie alignment?

James Taylor
In reply to this post by jjw14
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" <[hidden email]>  
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
>
>
> _______________________________________________
> galaxy-user mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user
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Re: Upload genome index to Galaxy for Bowtie alignment?

Kelly Vincent-2
In reply to this post by Kelly Vincent-2
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
>>>
>>>
>>> _______________________________________________
>>> galaxy-user mailing list
>>> [hidden email]
>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>
>

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Re: Upload genome index to Galaxy for Bowtie alignment?

Kelly Vincent-2
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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> galaxy-user mailing list
>>>>> [hidden email]
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>>
>>>
>>>
>>
>
>


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