Automating NGS Projects

With Basepair, you can fully automate an NGS project—create a project, add multiple samples, run analyses, and share everything with another user. Here are the steps:

0. Sign in to your Basepair account → https://{domain}/

1. Download your API config file — follow the steps in Setup to download it from your dashboard. Then make it available to the CLI using one of:

   # Option A — environment variable (persists for the session)
   export BP_CONFIG_FILE=/path/to/basepair.config.json
   
   # Option B — per-command flag
   basepair -c /path/to/basepair.config.json <subcommand>

2. Install the Basepair package

   pip install basepair

3. Create a new project for this data (note the returned project ID)

   basepair project create --name desired_project_name

4. Add your samples (note each sample ID)

   basepair sample create --name Treat_1   --genome hg19 --type rna-seq \
     --file1 /path/to/file1_R1.fq.gz --file2 /path/to/file1_R2.fq.gz
   
   basepair sample create --name Control_1 --genome hg19 --type rna-seq \
     --file1 /path/to/file2_R1.fq.gz --file2 /path/to/file2_R2.fq.gz
   
   # <add all your other samples>

5. Run differential-expression analysis (pipeline ID 8) using the sample and control IDs from step 4

   basepair analysis create --pipeline 8 \
     --sample 30754 30755 30756 \
     --control 30757 30758 30759

6. Share the project with another user (example: give edit permission; you can also use view or admin)

   basepair project update -u 1926 --team <team_id> \
     --emails collaborator@example.com --perm edit