Galaxy 101 tutorial

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Galaxy 101 tutorial

Carrie Gaut
I'm working my way through the Galaxy 101 tutorial. I've run into a discrepancy when trying to "Get Data" from the USC Main table browser. When trying to follow directions and choose the group, "variations and repeats," it doesn't exist. I can choose variations OR I can choose repeats. This makes several of the results not come out exactly as it shows they should and it makes steps further on in the tutorial confusing.

For me to get the correct tutorial results, which should I choose? Variations or repeats?

It may be that the tutorial was updated at some point but the tutorial directions and pictures were not. I hope I've posted this in the correct mailing list...

Sincerely,
Carrie
Sent from my iPhone
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Re: Galaxy 101 tutorial

Jen Hillman-Jackson
Hello Carrie,

Yes. UCSC changed the way that they organized their track groups,
breaking out Variation and Repeats into two distinct categories. When
doing the Table browser query, simply pick "Variation" (instead of
"Variation and Repeats") from the group drop down menu. The dbSNP track
will be there.

You mention that the results are slightly different - this is fine and
was already true. One of the datasets in the tutorial updates nightly
and the other every 2-3 months or so. Just use the most current versions
available and follow the instructions of how to do the analysis, the
exact numbers in the result will be the answer for the given inputs.

The goal of the tutorial is a general introduction to Galaxy - obtaining
data from external sources, using tools to manipulate, creating a
working, learning to share. Let us know if you have any other problems.

Best,

Jen
Galaxy team

On 4/20/14 6:11 PM, Carrie Gaut wrote:

> I'm working my way through the Galaxy 101 tutorial. I've run into a discrepancy when trying to "Get Data" from the USC Main table browser. When trying to follow directions and choose the group, "variations and repeats," it doesn't exist. I can choose variations OR I can choose repeats. This makes several of the results not come out exactly as it shows they should and it makes steps further on in the tutorial confusing.
>
> For me to get the correct tutorial results, which should I choose? Variations or repeats?
>
> It may be that the tutorial was updated at some point but the tutorial directions and pictures were not. I hope I've posted this in the correct mailing list...
>
> Sincerely,
> Carrie
> Sent from my iPhone
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org
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