I can't add TCGA data from a query to my project

Posted in TCGA data on the CGC by Mikki Behnke Tue Feb 16 2016 21:54:56 GMT+0000 (Coordinated Universal Time)·3·Viewed 780 times

I've joined today as a beta user and started a project, but once I do a query and pull up a list of files, I'm unable to highlight them either on the query map or the list of files in order to add them to my project for analysis. Is this a bug or am I doing something wrong? The help page indicates that I should be able to click on a path to highlight and add those files. Thanks!
Gaurav Kaushik
Feb 17, 2016

Hi Mikki,

I've created an example query to demonstrate how to add files to a project.

In this example, I've created a simple query that looks for all the RNA-Seq BAM files. When I've completed the query, you can see a table at the bottom listing each file: http://i.imgur.com/cbM5gtL.png

If I want to upload these data to a project, I click on one of the nodes. The 'Copy files to project' button at the top will then light up: http://i.imgur.com/1pO7WhM.png

I can then select one of your projects to add all the files from my query: http://i.imgur.com/RwDj8iw.png

If I go to the File Browser in that project, I see all the files have appeared: http://i.imgur.com/K9qTFkK.png

Please note that you can only add Controlled Access files (such as the ones in this query) to projects where you have indicated that Controlled Access data will be used. File permissions are discussed in the Data Browser documentation here: http://docs.cancergenomicscloud.org/docs/the-data-browser

Mikki Behnke
Feb 17, 2016

Thank you. It turned out that I had to add a condition of "Has files" to the filter before the clicking the node would activate the copy button.

Gaurav Kaushik
Feb 17, 2016

Thank you for updating us on the forum, Mikki!

  
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