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Tutorial

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 :ref:`this guide <install>`.

Running the CLI

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

.. toctree::
    cli

Estimating RNA velocity

This guide covers the analysis and assumes that you have produced a .loom file using the velocyto CLI (follow the guide above).

.. toctree::
    analysis