10x Genomics Cloud Analysis allows you to upload input files into your projects either using the 10x Genomics Cloud CLI (described below) or the Web Uploader.
The 10x Cloud accepts FASTQ sequence files from compatible sequencer platforms. Unsupported sequencing platforms may produce FASTQ file formats that are incompatible with the 10x Cloud.
What is the 10x Genomics Cloud CLI?
The 10x Genomics Cloud CLI is a command line tool that allows you to upload input files (custom references, FASTQ files, and images) to your 10x Genomics account, create projects from the command line, and manage other tasks related to your 10x Genomics account.
It is an executable that can be run directly and requires no compilation or installation.
The steps are operating system dependent. Please select the tab for your operating system below to continue.
Below is a step-by-step video demonstrating how to upload input files to 10x Genomics Cloud on a Windows operating system.
txg.exe files upload command instead of txg.exe fastqs upload. The workflow is otherwise identical.For a full reference of available commands and flags in the 10x Genomics Cloud CLI, visit the 10x Genomics Cloud CLI Documentation.
To upload files into a project, use the command provided in your project. You will also need to specify the project ID and the path to the input files.
- The project ID is a unique identifier that is automatically generated when you create a project. You can find the project ID in the upload command provided in your project.
- The path to the input files depends on where you saved them. For example, if you saved them in a subfolder called
FASTQswithin theDocumentsfolder, the path should look similar to:C:\Users\user.name\Documents\FASTQs. To easily copy the path for pasting into the command line, right-click on the folder of interest, select 'Show more options' in the context menu, and click on the 'Copy as path' button. This will copy the full path to your clipboard.
txg.exe files upload --project-id [insert unique project id] [insert path to input files]
Your FASTQ files must follow the Illumina naming convention, ex. SampleName_S1_L001_R1_001.fastq.gz.
Example upload commands
Below are three example commands for uploading input files to a project.
To upload all the input files in a given folder:
txg.exe files upload --project-id fo91F3f3jQTipjfGKpdV6lg myfastqs/
To upload a specific file:
txg.exe files upload --project-id fo91F3f3jQTipjfGKpdV6lg myfastqs/SampleName_S1_L001_R1_001.fastq.gz
To upload all the input files in a folder that begin with Sample01:
txg.exe files upload --project-id fo91F3f3jQTipjfGKpdV6lg myfastqs/Sample01*
Enter your access token
The first time you use the uploader, you will be prompted to provide an access token, which verifies your identity. The access token can be found in your Account Settings.
After verifying your identity, you will see a message similar to the following:
You are about to upload 3 file(s) to the following project
Project ID: 7e8fc23dd-fde3-4138-4138-f18aa5d57a96
Project Name: "My First Project"
Number of files: 3
/Users/your.name/myfastqs/test_sample_S1_L001_I1_001.fastq.gz (1.5 kB)
/Users/your.name/myfastqs/test_sample_S1_L001_R1_001.fastq.gz (2.9 kB)
/Users/your.name/myfastqs/test_sample_S1_L001_R2_001.fastq.gz (7.2 kB)
Total: 12 kB.
You will receive an email when the upload is complete.
To stop the upload, press Ctrl+C.
Proceed? [y/N]
Example success message:
Starting upload...
/Users/your.name/myfastqs/test_sample_S1_L001_I1_001.fastq.gz (1.5 kB) Done
/Users/your.name/myfastqs/test_sample_S1_L001_R1_001.fastq.gz (2.9 kB) Done
/Users/your.name/myfastqs/test_sample_S1_L001_R2_001.fastq.gz (7.2 kB) Done
Your upload has successfully completed!
You can view and analyze your data in the project "My First Project".
You will receive an email once the upload is complete. The email will be sent to the address associated with your 10x Genomics account. Once the upload is complete, go back to your project and start analyzing the uploaded files.