star-rnaseq-aligner

Included with Lifetime

$97 forever

STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics

General

What this skill does


# STAR RNA-seq Aligner Skill

## Purpose
Provide STAR alignment for splice-aware RNA-seq read mapping with comprehensive QC metrics.

## Capabilities
- Splice junction detection
- Two-pass alignment mode
- Chimeric read detection (fusions)
- Gene quantification (--quantMode)
- Custom genome index generation
- Output in multiple formats

## Usage Guidelines
- Generate genome indices with annotation
- Use two-pass mode for novel junction discovery
- Enable chimeric read detection for fusion analysis
- Generate quantification in addition to alignments
- Optimize parameters for read length
- Document STAR version and parameters

## Dependencies
- STAR
- HISAT2
- kallisto

## Process Integration
- RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)
- Spatial Transcriptomics Analysis (spatial-transcriptomics)

Files: 1

Size: 1.2 KB

Complexity: 9/100

Category: General

Source: https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/star-rnaseq-aligner

Related in General

modeling-omnistudio-epc-catalog

Included

Salesforce Industries CME EPC product-modeling skill for Product2-based catalog creation. Use when creating EPC products, configuring product attributes, building offer bundles with Product Child Items, or reviewing EPC DataPack JSON metadata for product catalog changes. TRIGGER when: user creates or updates Product2 EPC records, AttributeAssignment payloads, AttributeMetadata/AttributeDefaultValues, Offer bundles, or ProductChildItem relationships. DO NOT TRIGGER when: designing OmniScripts/FlexCards/Integration Procedures (use building-omnistudio-omniscript, building-omnistudio-flexcard, or building-omnistudio-integration-procedure), implementing Apex business logic (use generating-apex), or troubleshooting deployment pipelines (use deploying-metadata).

Generalscripts

relationship-science-coach

Included

Use this skill for direct, practical adult relationship coaching: couples conflict, repair, trust, marriage, dating, flirting, attachment patterns, emotional connection, sex, desire differences, eroticism, kink negotiation, affection, love languages, breakups, and long-term passion. Draw on Gottman, EFT and Hold Me Tight, attachment science, modern sex research, Perel, Nagoski, Kerner, Schnarch, Love and Stosny, and flexible love-language tools. Be concrete and low-hedge. Redirect only for imminent danger, abuse, coercive control, minors, non-consent, self-harm, stalking, or medical/legal/psychiatric decisions.

Generalscripts

building-sf-integrations

Included

Salesforce integration architecture and runtime plumbing with 120-point scoring. Use this skill to set up Named Credentials, External Credentials, External Services, REST/SOAP callout patterns, Platform Events, and Change Data Capture. TRIGGER when: user sets up Named Credentials, External Services, REST/SOAP callouts, Platform Events, CDC, or touches .namedCredential-meta.xml files. DO NOT TRIGGER when: Connected App/OAuth config (use configuring-connected-apps), Apex-only logic (use generating-apex), or data import/export (use handling-sf-data).

Generalscripts

venue-templates

Included

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.

Generalscripts

let-fate-decide

Included

Draws the 12 Houses of the Zodiac Tarot spread to inject entropy into planning when prompts are vague, ambiguous, or casually delegated. Interprets the spread to guide next steps. Use when the user says 'let fate decide', 'YOLO', 'whatever', 'idk', or other nonchalant phrases, makes Yu-Gi-Oh references, or when you are about to arbitrarily pick between multiple reasonable approaches. Prefer over ask-questions-if-underspecified when the user's tone is casual or playful rather than precision-seeking.

Generalscripts

net-ops

Included

Cross-platform network troubleshooting (Windows, macOS, Linux) via local or remote shell. Use for: DNS broken, can't resolve hostnames, nslookup/dig works but apps fail, NRPT, WFP, scutil, /etc/resolver, systemd-resolved, /etc/resolv.conf, NetworkManager, VPN DNS leak residue (ProtonVPN/Mullvad/WireGuard/AnyConnect), AV/firewall blocking DNS or DoH, Tailscale DNS interaction, intermittent connectivity, remote diagnostics over SSH.

Generalscripts