1. Help Center
  2. Videos
  3. 10X Genomics Single Cell RNA-seq

Setting Up your Cell Ranger Analysis

HubSpot Video


This tutorial video is a step-by-step guide to help you upload your 10X Genomics single-cell RNA-seq datasets through our Cell Ranger pipeline. If you prefer, you may also review our step-by-step guide below. 


Step-by-step guide: 

1. Create an experiment in ROSALIND by selecting "Add New Experiment" to an existing project folder or by selecting "Add New Project". 


Screen Shot 2021-04-23 at 12.16.13 PM 



2. Enter a Title and Description for your Project.

3. Select "Design a New Experiment" from the menu below. 


Screen Shot 2021-04-23 at 12.29.25 PM


4. Enter a Title and Description for your Experiment. 

5. Select your Method and Experiment Type from the drop down menus. 


Screen Shot 2021-04-23 at 12.37.06 PM


6. Select the species of your samples and the genome build from the dropdown menu. 

7. Specify the kit that was used for your samples from the dropdown menu. Select "Add Kit" to confirm. 


Screen Shot 2021-04-23 at 12.51.35 PM



8. Specify if any of your samples are replicates of one another. 

9. Specify attributes for each of your samples or upload an attribute file. You can find further instructions on how to create an attribute file here


Screen Shot 2021-04-23 at 6.42.37 PM

10. ROSALIND provides you with a sample sheet based on your specified attributes. You may make any changes you need directly on the sample sheet or, if all your attributes look correct, you can select "Next" to continue. 


Screen Shot 2021-04-29 at 11.54.42 AM


11. You may next set up your comparisons by selecting "Create New Comparison" and then dragging and dropping different attribute values into the condition and control boxes on the right hand side of your screen. This is an optional step as you may create an unlimited number of comparisons before or after your experiment has been launched.  


Screen Shot 2021-04-29 at 11.57.03 AM


12. Upload your FASTQs by dragging and dropping your FASTQ files onto ROSALIND. Once uploaded, your experiment will begin to launch! 


Screen Shot 2021-04-29 at 12.07.43 PM