Galaxy 101 Tutorial

Question: Galaxy 101 Tutorial

4.6 years ago by

Carrie Gaut • 50 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

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modified 2.1 years ago by Bob • 0 • written 4.6 years ago by Carrie Gaut • 50

4.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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" 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 workflow, learning to share. Let us know if you have any other problems.

Best, Jen

Reposted from galaxy-user@bx.psu.edu mailing list 4/21/14 8:14 AM

ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.1 years ago by

Bob • 0

United States

Bob • 0 wrote:

Comment:

For someone getting started with a "101" tutorial, it's really helpful if everything is exactly as it's advertised to be. Even little things like the difference between an item that says "variations and repeats" and two different items named "variations" and "repeats" causes a degree of uncertainty for a beginner. How many beginners have had that same question since this was posted 2.5 years ago? I know I did earlier this week. It's commonly known that for every person who asks a question, there are many others with the same question who don't ask it. They either struggle through to find an answer or give up.

So as a suggestion, it might be helpful for the Galaxy Project to provide their own simplified data server that matches their own tutorial (and not a tutorial on someone else's web site using data on yet someone else's site).

As a software developer myself, I know that it's difficult to keep dozens of tutorials up to date with constant user interface changes. But a "101 version" deserves the extra effort to make it match. After people become familiar with a tool, they're much more able to find their way around within outdated tutorials. But the first one (or 101) is important to get right.

ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by Bob • 0

Thank you for the feedback, it largely mirrors what the larger training community also found as areas to improve upon going forward.

If interested, there is a remote event to address training materials over the next few days. Perhaps you would like to join in / offer ideas?

Galaxy training contribution fest - 6-7th October https://github.com/bgruening/training-material/issues/58

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

Training materials almost always lag ongoing development. That's hard to avoid.

The Galaxy 101 tutorial suffered from the additional changes made to the data base - which weren't needed for the tutorial itself.

It's great to use real active databases, but having one that you control internally has its place as well.

So that would be my only contribution at this point.

Thanks very much for your kind help. We're just starting to use Galaxy for our work, and I'm sure I'll be asking for your help again.

ADD REPLY • link modified 2.1 years ago • written 2.1 years ago by Bob • 0

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