Creating Analyses

After you have uploaded FASTQ files into your project in Cloud Analysis, you are ready to analyze your data. A video guide that explains the analysis creation process is included below. If you would prefer to utilize a written tutorial, please skip the video and read the instructions that follow.

Jump to:
Video guide
Assigning library or feature types
Selecting files for analysis
Setting up your analysis

Video guide

Below is a step-by-step video demonstrating how to create a Cell Ranger analysis on 10x Genomics Cloud Analysis.


Assigning library or feature types

The FASTQ files that you have uploaded into your project have automatically been grouped into sets upon upload. In order to determine which pipeline is appropriate for your data, you must specify the library or feature type corresponding to the FASTQ sets that you are analyzing.

You may assign values one at a time using the dropdown selectors contained in each row of the table, highlighted in the screenshot below.

Individual assignment

If you have multiple FASTQ sets that share a library or feature type, you may select these rows in the table and apply a single library or feature type value to all selected rows using the selector that appears above the FASTQ file table, highlighted in the screenshot below.

Batch assignment


Selecting files for analysis

The Cell Ranger and Cell Ranger ARC pipelines, with the exception of the corresponding aggr pipelines, expect that all FASTQ files that are analyzed together are from a single GEM Well.

One or more sequencing libraries can be derived from a GEM Well. Additionally, one or more FASTQ sets can be generated for each sequencing library depending on the sequencing configuration. More details and examples can be found in the Cell Ranger documentation (for Single Cell Gene Expression and Immune Profiling data) and the Cell Ranger ARC documentation (for Multiome data).

In your project in Cloud Analysis, select the FASTQ sets that correspond to a single GEM Well and click the ‘Create New Analysis’ button to proceed.

Create analysis


Setting up your analysis

Depending on the types of data that are being analyzed, we will automatically open a setup form corresponding to our recommended pipeline for your data. By default, the newest versions are recommended. You may select older versions from the “Pipeline” field in the setup form.

Each field has a short description to explain the appropriate usage. If you need more information about any field, please consult the “Running Pipelines” pages of the Cell Ranger documentation (for Single Cell Gene Expression and Immune Profiling data) or the Cell Ranger ARC documentation (for Multiome data).

After entering values for all required fields and the appropriate optional fields, the “Run Analysis” button will be selectable. Clicking this button will initiate your pipeline run. Compute time will vary based on the size and types of data that you are analyzing, but typical runs take 1-2 hours. By default, you will receive an email notification when your analyses complete. If you would like to disable this notification, please update your preferences on your Account Settings.

After your analysis completes, you will be ready to download your output files. Learn more about downloading outputs.