QuagmiR on the Seven Bridges Cancer Genomics Cloud (CGC)

Create a CGC account and project

1. Create an account on the CGC.
2. Create a project.

Import data into your project.

3. Import data into your project using one of the following approaches:

• Upload your own data using the CGC Uploader (recommended) or other available tools
• Browse and select data from one of the publicly available datasets on the CGC using the Data Browsers

Copy QuagmiR to your project

4. Add the QuagmiR app to your project.

• Click on the Apps tab in your project.
• Click on + Add app.
• Browse for QuagmiR in the CGC Public Apps gallery.
• Click Copy to copy QuagmiR to your project.

Add a motif reference file to your project

5. Add a motif reference file to your project using one of the following approaches:

• Create your own file, and upload it to your project (see step 3).
• Copy the available motif_list_hsa.fa reference file into your project.
  • Click on the Files tab in your project.
  • Click on + Add app.
  • Browse for the file in the Public Reference Files.
  • Check the checkbox next to the file.
  • Click Copy to Project.

Run QuagmiR

6. Click on the Apps tab in your project.
7. Next to the QuagmiR app, click Run.
8. In the Set Input Data tab, select the desired fastq file(s) and motif reference file from within your project.

9. Edit the configuration of the run as needed in the Define App Settings tab.
10. Click on Run.

Create a custom QuagmiR workflow

11. If desired, use the CGC Workflow Editor to create a custom workflow that combines QuagmiR with other available bioinformatics tools.

Example workflow on the CGC that uses Picard SamToFastq to convert *.bam files into *.fastqfollowed by analysis of those files using FastQC Analysis and QuagmiR