Can I use this for quality control of sequencing replicates?

Yes, it includes specialized tools for multi-sample comparison, allowing you to generate PCA plots and Pearson/Spearman correlation heatmaps to verify replicate consistency.

How does the skill handle genomic normalization?

The skill provides precise guidance on applying RPGC (1x coverage), CPM, RPKM, and BPM normalization methods based on your specific experiment type and organism.

What sequencing types does this deepTools skill support?

It provides optimized workflows and commands for several high-throughput sequencing methods, including ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq.

Does it include genome size data for different species?

Yes, it contains a reference table of effective genome sizes for major organisms including Human (GRCh38), Mouse (GRCm38), Zebrafish, Drosophila, and C. elegans.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: Microck

byMicrock

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데이터 과학 및 ML

Processes and analyzes high-throughput sequencing data to generate publication-quality genomic visualizations and quality control metrics.

deepTools is a specialized Claude Code skill designed for bioinformaticians and researchers working with Next-Generation Sequencing (NGS) data. It provides expert guidance for transforming raw BAM alignments into normalized coverage tracks, performing rigorous quality control, and creating sophisticated genomic visualizations. Whether you are analyzing ChIP-seq, RNA-seq, or ATAC-seq data, this skill automates complex command-line workflows, ensures the use of correct normalization methods like RPGC or CPM, and provides standardized parameters for major model organisms to ensure reproducible and accurate genomic analysis.

주요 기능

01Seamless BAM to bigWig conversion with advanced normalization options

02High-resolution visualization tools for heatmaps and profile plots around TSS/peaks

03Specialized processing for ATAC-seq Tn5 shift correction and RNA-seq strand specificity

04Automated QC workflows including PCA, correlation, and fingerprint plots

0581 GitHub stars

06Pre-configured effective genome size references for Human, Mouse, and more

사용 사례

01Generating normalized signal tracks for publication-quality genomic visualization

02Profiling protein-DNA binding enrichment patterns around transcription start sites

03Assessing sequencing depth and replicate reproducibility across large NGS datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills deeptools

For use in Claude.ai and ChatGPT

Download Skill