skills.rest
tony-zhelonkin
tony-zhelonkinCOMMUNITY
Explore all skills by this author →
𝕏@TonyZhelonkinGitHub

starsolo-spliced-unspliced

Quantify spliced, unspliced, and ambiguous counts from FASTQ inputs using STARsolo Velocyto mode.

1|Updated Nov 20, 2025
Search Tags:#10x#scvelo#velocity-analysis#fastq#rna-velocity#starsolo#velocyto
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill starsolo-spliced-unspliced
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: starsolo-spliced-unspliced
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/starsolo-spliced-unspliced
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill starsolo-spliced-unspliced

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Quantifies spliced, unspliced, and ambiguous counts from FASTQ inputs using STARsolo Velocyto mode to accelerate RNA velocity workflows and provide velocity-ready output without a separate velocyto.py step.

Core Features & Use Cases

  • One-pass STARsolo Velocyto mode maps reads and quantifies Spliced, Unspliced, and Ambiguous counts in a single run for efficient velocity analysis.
  • Produces Velocyto-formatted output compatible with downstream tools such as scVelo, CellRank, and VeloVI.
  • Generates output structures compatible with downstream pipelines and enables CellRanger-compatible velocity layers when needed.
  • Supports common 10X chemistries (V3, V2, 5') and BAM input modes as described in the workflow.

Quick Start

Run STARsolo with --soloFeatures Gene Velocyto on your FASTQ data to generate velocity-ready spliced, unspliced, and ambiguous matrices in a single pass.

Frequently Asked Questions about starsolo-spliced-unspliced

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I quantify spliced and unspliced counts from FASTQ files for RNA velocity analysis?▼

This Skill uses STARsolo Velocyto mode to map reads and quantify spliced, unspliced, and ambiguous counts from FASTQ inputs in a single run, eliminating the need for a separate velocyto.py step.

What is the best way to generate RNA velocity matrices without running velocyto.py separately?▼

The best way to generate RNA velocity matrices without a separate velocyto.py step is using STARsolo's one-pass Velocyto mode to directly produce spliced, unspliced, and ambiguous count outputs.

Can I use STARsolo Velocyto output with scVelo and CellRank for RNA velocity?▼

Yes, STARsolo Velocyto output is compatible with scVelo, CellRank, and VeloVI, providing Velocyto-formatted spliced and unspliced matrices directly ready for downstream RNA velocity integration.

Does STARsolo Velocyto mode support 10x Genomics V3 and V2 chemistries?▼

Yes, STARsolo Velocyto mode supports common 10x chemistries including V3, V2, and 5' protocols, as well as BAM input modes for generating velocity layers.

How do I create CellRanger-compatible velocity layers from raw reads?▼

You can create CellRanger-compatible velocity layers from raw reads by running STARsolo with the Velocyto feature flag, which outputs compatible spliced, unspliced, and ambiguous matrices.

Related Skills

Explore More Data & Analytics Skills→
TianGzlabTianGzlab
155

genomics-alignment

Align FASTQ reads to reference genomes with BWA-MEM, Bowtie2, and Minimap2.

Official
Intermediate
tony-zhelonkintony-zhelonkin
1

rna-velocity-trajectory

Infer directional cellular trajectories from scRNA-seq using spliced and unspliced RNA ratios.

Community
Advanced
Zeyuyang-0420Zeyuyang-0420

scvelo

Infer cell state transitions from single-cell RNA-seq data using scVelo.

Community
Advanced
yf8578yf8578
1

scvelo

Perform RNA velocity analysis on single-cell RNA-seq AnnData objects.

Community
Advanced