Cell Ranger | Tutorial

1. Log In and Setup Your Project:

Access your Darwin account and navigate to your workspace. If you don’t have a workspace set up, create one by following the on-screen instructions.

2. Upload Your Data:

Go to the ‘Data’ section and upload your sequencing files, typically in the form of raw FASTQ files or a preprocessed BAM file. Ensure that your files are named correctly and organized as required for Cell Ranger.

3. Select Cell Ranger from the Tool Library:

Find Cell Ranger in Darwin’s library of analysis tools. You can use the search function to locate it quickly.

4. Configure Analysis Parameters:

Configure the analysis parameters in Cell Ranger. You will need to specify the type of analysis (e.g., count, vdj, or aggr), reference genome, and any other options that are critical for your specific analysis needs. Input the expected number of cells, if known, and any other specific parameters that your experiment requires.

5. Run Cell Ranger, Interpret Results:

Submit the job to run. This process may take some time depending on the size of your data and the complexity of the analysis. Once the analysis is complete, review the output files. Cell Ranger will generate various output files including feature-barcode matrices and analysis reports that can be used for further biological interpretation.