Velocyto consists of two main components:

  • A command line interface (CLI), that is used to run the pipeline that generates spliced/unspliced expression matrices.
  • A library including functions to estimate RNA velocity from the above mentioned data matrices.

Getting Started

First make sure that velocyto is correctly installed following this guide.

Running the CLI

This guide explains how to run the counting pipeline. This starts from .bam/.sam files and yields a .loom file with counts divided in the categories spliced/unspliced/ambiguous.

Estimating RNA velocity

This guide covers the analysis and assumes that you have produced a .loom file following the guide above.