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Velocyto Specifications

Process Details

  • Name: velocyto
  • Process UUID: 4b386949d7c94820b56791fd70a7de00
  • Process Group: SingleCell

Overview

Velocyto is a single-cell RNA velocity analysis tool that estimates the rate of gene expression change by analyzing spliced and unspliced mRNA molecules in single-cell RNA-seq data. This process generates velocity estimates that can be used to infer the future state of individual cells and reconstruct developmental trajectories.

This process is implemented in Bash, which invokes the Velocyto Python tool for RNA velocity analysis.

Key Functionality

  • RNA Velocity Estimation: Calculates RNA velocity by quantifying spliced and unspliced transcript abundances from single-cell BAM files
  • Cell Barcode Integration: Processes cell barcode information to associate velocity estimates with specific cells
  • GTF-based Annotation: Uses gene annotation files to distinguish between intronic and exonic reads for velocity calculations
  • Loom Output Generation: Produces standardized loom files containing velocity data for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • BAM File Set

    • Description: Aligned single-cell RNA-seq reads in BAM format containing cell barcode and UMI information
    • Format: BAM

  • Input File TSV Set

    • Description: Tab-separated file containing cell barcodes and associated metadata
    • Format: TSV

  • GTF File

    • Description: Gene annotation file in GTF format used for transcript structure annotation
    • Format: GTF

Optional Inputs

  • GTF File (Mask)
    • Description: Optional masking GTF file to exclude specific genomic regions from velocity analysis
    • Format: GTF

Outputs

  • Loom File
    • Description: Contains RNA velocity estimates, spliced/unspliced count matrices, and cell metadata in loom format
    • Format: LOOM

Parameters & Settings

This process is conditionally executed based on the run_velocity parameter configuration in the workflow.

References & Resources

  • Tool Documentation: Contact the team for details on the Velocyto implementation
  • Related Papers: La Manno, G. et al. RNA velocity of single cells. Nature 560, 494-498 (2018). https://doi.org/10.1038/s41586-018-0414-6