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.
For the easiest functionality, 10x Genomics recommends using the Web Uploader. For uploading large numbers of input files, it is recommended to use the Cloud CLI.
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 macOS operating systems. Linux users will find the installation and usage instructions nearly identical to macOS users.
txg files upload
command instead of txg fastqs upload
. The workflow is otherwise identical.Download the 10x Genomics Cloud CLI for your operating system and unpack it to a convenient location. Make sure you download the 10x Genomics Cloud CLI for the operating system where your data lives. Your home directory is a good default location.
Optionally, install the binary in a location where you can execute it globally (e.g., /usr/local/bin
).
If you’re using a Linux system, use the command below to download:
curl -f -o txg-linux-v2.0.0.tar.gz https://cf.10xgenomics.com/cloud-cli/v2.0.0/txg-linux-v2.0.0.tar.gz
and then to unpack:
tar -zxvf txg-linux-v2.0.0.tar.gz
To run the 10x Genomics Cloud CLI, you need to enter the path to the executable.
Option 1: You can navigate into the executable's directory, for example txg-linux-v2.0.0
, and run the command from within the directory every time you want to run a command. For example:
cd /home/user.name/apps/txg-linux-v2.0.0/
./txg help
Option 2: Or you can specify the full path to the executable every time you want to run a command. For example:
/home/user.name/apps/txg-linux-v2.0.0/txg help
Option 3: Or you can add the txg executable to your $PATH
. This means you can type txg [command]
from anywhere to access the executable and run commands. If you use the echo
command below, you should see a list of directories separated by colons similar to below.
echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/go/bin
If you put the 10x Genomics Cloud CLI executable in one of these directories, you've added it to your $PATH
and can run the txg
command from anywhere. There are several ways to add an executable to your $PATH
. Here's one method:
First, navigate into the directory you just downloaded and unpacked.
cd txg-linux-v2.0.0/
Then print the path to current directory using this command:
pwd
The output should be the directory containing the txg executable. Copy the outputted path and use it in the following export
command to add it into the $PATH
variable.
export PATH=[directory containing the executable]:$PATH
For example:
export PATH=/mnt/home/user.name/yard/apps/txg-linux-v2.0.0:$PATH
To verify you correctly added the 10x Genomics Cloud CLI to your $PATH
, enter:
which txg
You should see output similar to the following:
/mnt/home/user.name/yard/apps/txg-linux-v2.0.0/txg
Note: this only temporarily adds the executable to your $PATH
. It's only valid in the current shell session. To permanently add txg
to your $PATH
, add the export
command you just used to your .bashrc
(Linux) or .zshrc
(macOS v10.15+), which is a special script that runs everytime you login to your system. For more details, view this tutorial.
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
FASTQs
within theDocuments
folder, the path should look similar to:/Users/user.name/Documents/FASTQs
. To easily copy the path for pasting into the command line, right-click on the folder of interest and select 'Copy<folder-name>
' in the context menu. This will copy the full path to your clipboard.
./txg files upload --project-id [insert unique project id] [insert path to inputs]
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 files in a given folder:
./txg files upload --project-id fo91F3f3jQTipjfGKpdV6lg myfastqs/
To upload a specific file:
./txg files upload --project-id fo91F3f3jQTipjfGKpdV6lg myfastqs/SampleName_S1_L001_R1_001.fastq.gz
To upload all the files in a folder that begin with Sample01
:
./txg 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.
For a full reference of every command and flag available in the 10x Genomics Cloud CLI, visit the 10x Genomics Cloud CLI Documentation.