ambient-rna-triage

name	ambient_rna_triage
description	Triage whether ambient RNA contamination is a plausible explanation for suspicious single-cell expression patterns.
category	bio/single_cell_rna
version	1
requires_tools	["search_knowledge_base","python_repl"]
requires_network	false
user_invocable	true
tags	["ambient-rna","soup","contamination","triage"]
aliases	["ambient_contamination_check"]
species	any
modality	single_cell_rna
stage	qc
stability	stable
safety_level	low

Ambient RNA Triage

Purpose

Assess whether ambient RNA contamination is a likely contributor to unexpected marker expression or noisy cluster interpretation.

When to use

Use this skill when the user reports improbable marker expression, broad low-level contamination, or suspicious signals in droplet-based single-cell data.

Required inputs

• observed problem: for example unexpected markers across many clusters
• data context: droplet-based or not, sample quality, and any known QC issues
• suspect genes (optional)

Steps

1. Search knowledge/ambient-rna-troubleshooting.md with search_knowledge_base.
2. Compare the reported symptoms against common ambient RNA patterns.
3. Distinguish ambient RNA from related explanations such as doublets or real activation states.
4. Use python_repl only if you need to organize a checklist or risk table.
5. Recommend next checks such as low-count cell review, marker sanity checks, or SoupX/CellBender.

Output format

• Assessment: suspected, plausible, or not strongly supported
• Why
• Most informative next checks
• Main interpretation risk

Failure modes

• Too little context: ask whether the data are droplet-based and which genes look suspicious.
• Strong alternative explanation: say ambient RNA is not the main hypothesis.
• No suspect genes given: keep the answer high-level and diagnostic.

Examples

• "Could ambient RNA explain albumin expression across unrelated cell types?"
• "I see low-level hemoglobin genes in many cells. Is this ambient contamination?"