CELLRANGER COUNT - aces/cbrain GitHub Wiki

Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. To know more about Cell Ranger please visit 10xgenomics!

This section gives you a step-by-step process of the Cellranger count tool.

• Select Create Project

A new window will pop up, allowing you to enter the name and description of your project

• Click Create
• CBRAIN will confirm the project creation
• The new project will be available on your Projects list view
• You can invite others to join by clicking on Edit

There are four ways to Transfer data in and out of CBRAIN:

• Transfer files one by one using the Web browser (works only for small files)
• Upload or download files using a SFTP client to a special Data Provider
• Ask the CBRAIN admins to configure one or several Data Providers directly on a user's machine or at a user's lab.
• Configure a personal Data Provider (CBRAIN)

• File requirement: file(s) has to be registered as a FASTQ collection.

• Select your FASTQ Collection file(s).

For the purpose of this tutorial, the data have been downloaded directly from 10xgenomics and available here.

Note: In most cases, more than one file is needed to run your Cellranger project. However, new collection creation will not be required if you only use one file. Simply select the file and launch the task as it is.

• Launch

Click on the Launch button, select the tool, execution server and the version then Launch cellranger count

If you want to run a quick run test, we recommend selecting Converter-1 or Converter-2.

• Task parameters settings

1. Choose the data provider where you want to save your results (for example MainStore)
2. Choose your project
3. Set up your Task parameters (transcription path and FASTQS data and prefix)

Once the task is running, you will get a notification advising the task is launched

• click on Tasks to monitor the status of your task(s)

• Once your task is completed (or failed), you will get a new notification

• Go back to your task (by clicking on the task name) where you can see the information of your task including the input and output results

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• Click on the Output files to view your results

• Expand the outs file, as an example click on the web_summary_html and you will see the Cell Ranger counts results of your task