Making a Data Request
St. Jude Cloud does not allow for-profit companies to access any restricted access genomics data. We are actively working with our institution to assess the feasibility of providing data to for-profit entities. If you work for a for-profit company and would like to be notified if this restriction changes, feel free to email us at email@example.com.
Request Process Overview¶
Creating a data request is the premier way to access raw St. Jude next generation sequencing data in the cloud. You can get a free copy of the data in a secure cloud environment powered by Microsoft Azure and DNAnexus, or you can elect to download the data to your local computing environment.
Helpful Things to Remember:¶
- Data in St. Jude Cloud is grouped into Data Access Units (DAUs), which usually correspond to large-scale sequencing initiatives at St. Jude.
- Individuals can apply for access to DAUs on a case-by-case basis for a specific amount of time (usually 1 year).
- Access to data in a given DAU is assessed by the corresponding Data Access Committee who reviews a variety of factors to grant access.
The primary way to make your data selection is through our Genomics Platform Data Browser. You can search our raw genomic data by diagnosis, publication, or study by selecting a tab along the top. You may further refine your search by applying filters from four categories: Sequencing Type, Sample Type, File Type, and Tissue Type. Please note that applying multiple filters within the same category filters using 'OR' logic while applying multiple filters across different categories filters using 'AND' logic. For example in the overview image above, we have filtered the browser to only show data that is (either WGS OR WES) AND (Diagnosis OR Relapse) AND BAM AND Paired Tumor-Normal.
As you filter and make selections, the data summary panel in the upper left hand corner will update dynamically to give you important descriptive information about the set of data you have selected. Click on an empty box to make a selection; when selected, the box will turn blue with a white check mark. Once you have completed your data selection, click on Request Data to submit your request and proceed.
You must have created an account and be logged in to submit a data request. If you have not yet created an account or you are not logged in, the submit button will say Log In rather than Request Data.
Alternatively, you may be directed to the Genomics Platform Data Browser through another App to request specific samples. The PeCan homepage is one such app that allows you to select data through an interactive visualization.
After clicking on Request Data, we ask that you review your selection and make sure that the DAUs corresponding to the set of data you have selected is indeed the data you want to request.
Making the Request¶
Now that you have selected your data, you will need to fill in some information to complete the request. From here, necessary information will be collected through a setup wizard. All of your progress will be automatically saved, and you can follow along with your progress on the left sidebar.
This information will be collected whether you are requesting open-access or controlled-access data. It helps us structure your project folder correctly when we vend the data to you.
Signing the Data Access Agreement¶
If you already have access to the data or are requesting open-access data, you will not be prompted to go through this section.
Every person who requests access to our controlled-access data must sign the Data Access Agreememnt (DAA). If you are located in the United States of America, you can opt in to completing the DAA through an electronic setup wizard. If you are not located in the USA, or would like to complete the form manually, you can follow our instructions on Filling Out The Data Access Agreement.
If you opt to do the process through the setup wizard, the necessary information will be collected and added automatically to your agreement. Once you have completed the setup wizard, the form will be sent to you and necessary signatories through email via DocuSign. You can learn more about our electronic data access agreement process here.
Request approval typically takes a week or two if your data access agreement is correctly and completely filled out. You will receive automated emails from firstname.lastname@example.org at the time that your request is approved.
If you receive an email from us that your DAA is incomplete, you may edit your DAA and upload the revised copy using the 'Add a Form' button the on My Dashboard page.
Managing your Data Request¶
Go to our Managing Data Overview documentation page to learn how to check the status of your data request, complete an EDAA draft, upload a revised DAA, and ultimately access your data from your My Dashboard page.
If you would like to download the data to local storage, there are extra steps you'll need to follow such as getting additional signatures on your data access agreement. We recommend that you work with the data in the cloud if it's feasible; the data provided by St. Jude is free, the compute charges are reasonable, and working in the cloud helps to eliminate the long, error-prone downloading process. Porting your tools to be run in the cloud is easy, as well. We recommend you follow this guide to get started.