# Accessing HTAN open access data stored in Synapse via SB-CGC

HTAN’s open-access data, including most datasets, is hosted on Synapse and can be loaded into the SevenBridges Cancer Genomics Cloud using the following instructions. Note that open-access Level 2 images are available separately through the Cancer Data Service (CDS).

# Video walkthrough

Watch video walkthrough on Zoom

# Step-by-Step Guide

# 1. Start a Data Studio Instance

Go to CancerGenomicsCloud.org.
Log in and launch a Data Studio instance with JupyterLab.

# 2. Install and Configure Synapse Client

Open the Terminal in JupyterLab.
Install the Synapse client (if not already installed) by typing:
```
pip install synapseclient
```
Obtain a Personal Access Token:
- Log into Synapse.org.
- Go to Account Settings > Personal Access Tokens.
- Create a new token with “View and Download” permissions and copy the token.
Configure Synapse client with the Token:
- In the JupyterLab Terminal, type:
```
synapse config
```
- When prompted, enter your Synapse username (optional) and paste the token.

# 3. Select Files from the HTAN Data Portal

Visit the HTAN Data Portal and find the data files you need (e.g., single-cell RNA-seq data in H5AD format).
Click the purple “Download selected files” button for the chosen files.
Copy the download commands (e.g., synapse get syn1234).

# 4. Download Files into the Data Studio Instance

Paste the copied download commands into the JupyterLab Terminal.
Verify that the files are in the workspace directory. You can now use these files within notebooks in the Data Studio instance.

# 5. Move Files to Output Folder

Move files to the output-files directory to ensure they sync with your CGC project:
```
cp <filename> ../output-files
```

# 6. Stop Data Studio Instance

Stop the Data Studio instance to trigger synchronization.
Check your project files on CGC; the downloaded files should now be available for further use.