Can this skill help convert BAM files to bigWig format?

Yes, it provides optimized command-line patterns for bamCoverage and bamCompare, including specific normalization methods like RPGC and CPM.

How does this skill handle ATAC-seq specific requirements?

It provides specific instructions for Tn5 offset correction using alignmentSieve and fragment size analysis to identify the characteristic nucleosome ladder pattern.

Does it include normalization guidance for different organisms?

Yes, it contains a reference guide for effective genome sizes for Human (hg38), Mouse (mm10), Zebrafish, Drosophila, and C. elegans to ensure accurate RPGC normalization.

Can I use this to generate publication-quality plots?

Absolutely. It covers the full visualization pipeline from computeMatrix to plotHeatmap and plotProfile, including color mapping and clustering options.

What sequencing data types does this skill support?

The deepTools skill supports a wide range of High-Throughput Sequencing (NGS) data types, including ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: ricable

byricable

•

Data Science & ML

Processes and visualizes high-throughput sequencing data to generate publication-quality genomic insights and quality control reports.

This skill equips Claude with the expertise to manage and analyze Next-Generation Sequencing (NGS) data using the deepTools suite. It provides specialized guidance for ChIP-seq, RNA-seq, and ATAC-seq workflows, including BAM to bigWig conversion, sample correlation, and PCA. Users can leverage this skill to generate standardized visualization matrices for heatmaps and profile plots around genomic features, ensuring high-quality data normalization and rigorous quality control for bioinformatics research.

Key Features

01Advanced visualization of genomic features via heatmaps and profile plots

021 GitHub stars

03Normalized BAM to bigWig/bedGraph conversion using RPGC, CPM, or RPKM

04Tailored workflows for Tn5-corrected ATAC-seq and strand-specific RNA-seq

05Comprehensive QC tools for sample correlation, PCA, and sequencing depth assessment

06Integrated reference library for effective genome sizes across common organisms

Use Cases

01Performing quality control and reproducibility checks on sequencing replicates

02Generating publication-ready heatmaps of ChIP-seq signal enrichment around TSS regions

03Creating normalized coverage tracks for comparative analysis between treatment and control samples

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent deeptools

For use in Claude.ai and ChatGPT

Download Skill