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 this guide.

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.

• CLI Usage Guide
  • Introduction
  • Preparation
    • Download genome annotation file
    • Download expressed repeats annotation
  • Running velocyto
  • run10x - Run on 10X Chromium samples
  • run_smartseq2 - Run on SmartSeq2 samples
  • run_dropest - Run on DropSeq, InDrops and other techniques
  • run - Run on any technique (Advanced use)
    • Notes on first runtime and parallelization
    • Run with different logics
  • Requirements on the input files
  • About the output .loom file
    • Merging multiple samples/lanes in a single file
  • Get started with the analysis

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).

• Analysis Pipeline
  • Velocyto Loom
  • Start a new analysis - Preliminary Filtering
  • Preparation for gamma fit
  • Gamma fit and extrapolation
  • Projection of velocity onto embeddings