Question: Data analysis workflow in Galaxy
0
gravatar for maki.dur
3.0 years ago by
maki.dur0
Croatia
maki.dur0 wrote:

Hello to everyone,

I am quite new in bioinformatics and I need little help. I got task to implement a data analysis workflow in Galaxy platform for data coming from variant search DNA-Seq experiment sequenced with Illumina HiSeq Instrument. Can someone, please give mi some instruction how to start with it? I found a lot of tutorials, but the most of them only confusing me. Another problem is that I am a bit "short" with time, as DL for task is tomorrow :(.

Thanks in advance,

Marija

 

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by maki.dur0
1
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The easiest way to create a workflow is to just go ahead and create the analysis path in your History, then extract the Workflow. From there, you can edit it to add in annotations and other customizations. Examples can be found on http://usegalaxy.org under "Shared Data -> Published Histories or Workflows".

A few "Published Pages" will also be helpful, so search in there. This one is a supplemental for a Galaxy publication that covers various analysis paths (including simple variant analysis) and workflow creation: https://usegalaxy.org/u/galaxyproject/p/ngs-analysis-2013

Please be aware that older Workflows will in several cases not run "as is". These can be tuned, but it is sometimes quickest to just follow the methods you decide to use (your own, or from a publication, or from the tool author's manual), execute the protocol new in a History tuned to match your data inputs, then extract/create your own Workflow. Galaxy just went through a major tool and engine upgrade and will continue to evolve. 

Documentation to cover all recent changes is still in progress, as these changes are still in progress. A new publication from the Galaxy team in coordination with our community is in progress that will cover several core analysis pipelines using the latest tools and methods. But, this is still some time away from being completed/published. Once done, a supplemental will be available under the Shared Data locations, plus the publication itself will be available along with an external server and a cloud share that is configured for executing the protocols. 

Doing this all in a day on the public server is a bit tight on time. Larger jobs will execute under quota guidelines. If this is really your deadline, a cloud Galaxy could be a better choice, but that too will take some time to configure and use. And if you wanted to apply to AWS for a research grant to cover costs, that takes some time to process. 

There are other Galaxy resources, but it sounds as if you have reviewed those. Others are welcome to add in more.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for maki.dur
3.0 years ago by
maki.dur0
Croatia
maki.dur0 wrote:

Dear Jen,

Thanks for the explanation. It helps me a lot.

Marija

 

ADD COMMENTlink written 3.0 years ago by maki.dur0
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