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
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
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
Hello,
Here is some help: https://genome-cancer.ucsc.edu/proj/site/help/#download
Thanks, Jen, Galaxy team
