Automating NGS projects

Modified on Wed, 17 Jul at 5:18 AM

With Basepair, you can fully automate a NGS project. Create a new project, create multiple samples in the project, run multiple analysis and then share the whole project with another user. Here are the steps.

0. Sign in to your Basepair account - https://{domain}/, if you haven't already!

1. Download your API keys from https://{domain}/api/v3/users/api_key/ and save path of the downloaded file in an env var

(Note: Login to your account for downloading the JSON file)

export BP_CONFIG_FILE=/path/to/basepair.config.json

2. Install basepair package

pip install basepair

3. Create a new project for this data. Please note the project id.

basepair create project --name desired_project_name

4. Add your samples and note the sample ids.

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>

5. Run differential expression analysis (workflow # 8). Please use the sample and control id from step 4.

basepair create analysis -w 8 --sample 30754 30755 30756 --control 30757 307587 30759

6. Share project with another user. In this example, the other user gets edit permission. You may also give view or admin permissions.

basepair updateProject -p 1926 --emails amit@basepairtech.com --perm edit