👤 Analysis by: Vishnu Kumar and Marek Bartkuhn
scRNA-seq Analysis Using Illumina DRAGEN Pipeline
- Make an account on Illumina BaseSpace: https://login.illumina.com/platform-services-manager/?rURL=https://basespace.illumina.com&clientId=basespace&clientVars=aHR0cDovL2Jhc2VzcGFjZS5pbGx1bWluYS5jb20vZGFzaGJvYXJk&redirectMethod=GET#/register
- Here, we can create different projects. Within a specific project, we can upload files either by drag-and-drop or using the CLI.
- To run a specific app, go to the Apps tab and type "single cell". This will display the DRAGEN Single Cell RNA app. Click on it to open this app, where you can view pipeline information, input file requirements, and other relevant details. Then click Launch Application, select the required input files and parameters, and run the analysis.
Install BaseSpace Sequence Hub CLI
Documentation: https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview
Installation for Linux is given below.
Installation for Linux
# make directory
$ mkdir -p $HOME/bin
$ wget "https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs" -O $HOME/bin/bs
# file permissions
$ chmod u+x $HOME/bin/bs
Authenticate to EU server
$ bs auth --api-server https://api.euc1.sh.basespace.illumina.com
You will get a URL — paste it into a browser to complete authentication.
Inspect the token
$ bs whoami
Configure the server to EU
$ eval $(bs load config eu)
# list projects
$ bs list projects
# list app sessions
$ bs list appsession
Command-Line Reference
https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-examples#FASTQupload
Upload and download files
# upload folder /files
$ bs upload dataset -p <ProjectID> --recursive .
# download a complete project
$ bs download project -i <ProjectID> -o <output>
# download specific data
$ bs download appsession --id <APPSESSION_ID> --output <LOCAL_FOLDER>