Question: How get Cancer WGS for analysis in Galaxy
0
gravatar for AlexTall
2.9 years ago by
AlexTall0
AlexTall0 wrote:

Hi,

 

I want to do some analysis on Whole Cancer Genome data.

1) Can I get the sequence form some section in “Get Data” or does it needs to be uploaded into Galaxy.

2) If the sequence needs to be uploaded from where I should get it and how upload it to the Galaxy.

 

Thank you in advance for your help

 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by AlexTall0
3
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Galaxy is not a data repository specifically, more of an analysis tool kit. To obtain data, and you know the study of interest, it may well be in the EBI SRI repository. There is a tool under "Get Data" to import data from this source directly. That said, any data in a suitable format can be uploaded through the "Upload File" tool.

The UCSC Cancer browser is also a great resource. It makes use of both Galaxy and the core UCSC Genome browser resources, and has some customized analysis methods and tools for this type of work. https://genome-cancer.ucsc.edu/ Other public Galaxy browsers also have a cancer analysis focus.

There are also analysis resources in our wiki and at the main public Galaxy web site. See:
http://galaxyproject.org -> Learn -> Tutorials, Events, Train, Choices (other public Galaxy sites)
http://usegalaxy.org -> Pages

Hopefully this helps to get you started, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson23k
0
gravatar for AlexTall
2.9 years ago by
AlexTall0
AlexTall0 wrote:

Dear Jennifer,

Thanks for your informative reply.

I found EBI SRI repository a very good and easy to use database. Though I cannot handle to use "UCSC Cancer browser" for uploading data in to Galaxy, despite my efforts.

I will appreciate if you help me to know how upload data from "UCSC Cancer browser" into Galaxy.

 

All the best

ADD COMMENTlink written 2.9 years ago by AlexTall0

Hello,

Here is some help: https://genome-cancer.ucsc.edu/proj/site/help/#download

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson23k
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