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:

Sign in to your Basepair account → https://{domain}/
Download your API keys from https://{domain}/api/v3/users/api_key/ and save the path of the downloaded file in an environment variable
(You must be logged in to download the JSON file.)
```
export BP_CONFIG_FILE=/path/to/basepair.config.json
```
Install the Basepair package
```
pip install basepair
```
Create a new project for this data (note the returned project ID)
```
basepair create project --name desired_project_name
```

Add your samples (note each sample ID)

basepair create sample --name Treat_1   --genome hg19 --datatype rna-seq \
  --file1 /path/to/file1_R1.fq.gz --file2 /path/to/file1_R2.fq.gz

basepair create sample --name Control_1 --genome hg19 --datatype rna-seq \
  --file1 /path/to/file2_R1.fq.gz --file2 /path/to/file2_R2.fq.gz

# <add all your other samples>

Run differential-expression analysis (workflow # 8) using the sample and control IDs from step 4
```
basepair create analysis -w 8 --sample 30754 30755 30756 --control 30757 307587 30759
```
Share the project with another user (example: give edit permission; you can also use view or admin)
```
basepair updateProject -p 1926 --emails amit@basepairtech.com --perm edit
```