downloading reference sequences and other questions

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downloading reference sequences and other questions

Joanne Rampersad
Hi
I have a few questions

1. I am trying to use Bowtie to map my data using a reference genome.
the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is
there a way that I can download the file in fasta format to use as a
reference in Tablet?

I can import the SAM output into Tablet if I do not give it a
reference, but I would like to see it with the reference

2. I have used the Sam to Bam converter and downloaded the file to my
computer then tried to import it into Tablet, but it gives an error.
Does anyone have any advice on doing this?

3. Does Galaxy have any tools for doing a blast search against a
reference genome or database?

Any help/instructions that you point me to is greatly appreciated.


Jo
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Re: downloading reference sequences and other questions

Anton Nekrutenko
Joanne:

1. There is no mechanism for downloading reference sequences from Galaxy at this time.
2. I am not sure what you mean by 'Tablet'.
3. Megablast tool ('NGS: Mapping -> Megablast') will allow you to perform comparisons against nt, wgs, and htgs databases.

Thanks for using Galaxy,

anton
galaxy team


Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Jun 22, 2011, at 4:15 PM, Joanne Rampersad wrote:

> Hi
> I have a few questions
>
> 1. I am trying to use Bowtie to map my data using a reference genome.
> the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is
> there a way that I can download the file in fasta format to use as a
> reference in Tablet?
>
> I can import the SAM output into Tablet if I do not give it a
> reference, but I would like to see it with the reference
>
> 2. I have used the Sam to Bam converter and downloaded the file to my
> computer then tried to import it into Tablet, but it gives an error.
> Does anyone have any advice on doing this?
>
> 3. Does Galaxy have any tools for doing a blast search against a
> reference genome or database?
>
> Any help/instructions that you point me to is greatly appreciated.
>
>
> Jo
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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Re: downloading reference sequences and other questions

Jen Hillman-Jackson
In reply to this post by Joanne Rampersad
Hello Jo,

Please see below

On 6/22/11 1:15 PM, Joanne Rampersad wrote:

> Hi
> I have a few questions
>
> 1. I am trying to use Bowtie to map my data using a reference genome.
> the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is
> there a way that I can download the file in fasta format to use as a
> reference in Tablet?
>
> I can import the SAM output into Tablet if I do not give it a
> reference, but I would like to see it with the reference

Galaxy does not currently have genomes available for download. Good
sources would be UCSC, NCBI, Ensembl, and other species-specific projects.
>
> 2. I have used the Sam to Bam converter and downloaded the file to my
> computer then tried to import it into Tablet, but it gives an error.
> Does anyone have any advice on doing this?

The best folks to answer Tablet questions would be those tool authors,
but that said, a some guesses are that the .bam.bai index file was not
loaded along with the .bam? Or maybe the SAM needed to be sorted in some
special way first?
>
> 3. Does Galaxy have any tools for doing a blast search against a
> reference genome or database?

BLAST is not in on the Galaxy main server, but if you want to see how it
is incorporated, it is on our test server (but beware if running any
serious jobs, this is an active development area and large runs are not
permitted). http://test.g2.bx.psu.edu. After testing out the
implementation, and you decide that you want to run BLAST on full
datasets using Galaxy, then creating a cloud or local instance is the
recommendation.
http://getgalaxy.org
http://getgalaxy.or/cloud


Hopefully this is helpful! Thanks for using Galaxy!

Best,

Jen
Galaxy team

>
> Any help/instructions that you point me to is greatly appreciated.
>
>
> Jo
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/
Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: downloading reference sequences and other questions

Jen Hillman-Jackson
Link correction:

> http://getgalaxy.or/cloud

should be http://usegalaxy.org/cloud

With the two answers from our team to (hopefully) help, we wish the best
for your project,

Jen
Galaxy team
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/
Jennifer Hillman-Jackson
http://galaxyproject.org