How to Run a New Analysis on Basepair

To run a new analysis, make sure you have uploaded the samples you want to analyze. If you’re not sure how to do that, see our previous tutorial on how to add a sample to Basepair.

1. Hover over the Analysis tab at the top and click New Analysis.
2. Choose the pipeline you want to run.
3. Select the sample or samples you want to analyze.
4. Feel free to change the analysis name as needed.
5. (Optional) If you’re an advanced user and want to customize your analysis parameters, click Change default options.
6. Finally, click Run Analysis.

The time it takes to run an analysis depends on the pipeline, ranging from about 30 minutes for a differential expression analysis to a few hours for a single-cell RNA-seq analysis.

If you’re running multiple analyses at once, this won’t slow anything down—Basepair spins up servers on demand, so all analyses run in parallel.