What file formats does the deepTools skill support?

It primarily processes BAM, bigWig, bedGraph, and BED files, which are the standard formats for high-throughput sequencing data and genomic intervals.

What normalization methods are available?

The skill supports various methods including RPGC (1x genome coverage), CPM (Counts Per Million), RPKM, BPM, and raw count normalization.

Can I use it to compare treatment vs. control samples?

Absolutely. It features tools like bamCompare specifically designed to calculate log2 ratios or differences between two samples to highlight areas of differential enrichment.

How does it assist with Quality Control (QC)?

It provides commands for generating PCA plots, correlation heatmaps, fingerprint plots for ChIP enrichment, and fragment size distributions to ensure data reliability before downstream analysis.

Can this skill help with RNA-seq specific workflows?

Yes, it includes specialized guidance for RNA-seq, such as generating strand-specific coverage tracks and using appropriate normalization methods like RPKM while avoiding read extension over splice junctions.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: Microck

byMicrock

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データサイエンスとML

Analyzes high-throughput sequencing data (NGS) through automated quality control, normalization, and publication-quality visualization.

deepTools is a specialized toolkit designed for processing BAM, bigWig, and BED files to extract biological insights from high-throughput sequencing experiments. This skill provides Claude with domain-specific knowledge to perform sophisticated normalization, sample comparisons, and generate visualizations like heatmaps and profile plots. It is particularly useful for bioinformatics researchers and computational biologists working on ChIP-seq, RNA-seq, and ATAC-seq workflows who need to transform raw alignment data into interpretable genomic signals.

主な機能

01Performs multi-sample quality control including PCA and correlation analysis

02Calculates ChIP-seq enrichment strength using fingerprint plots

03Provides specialized workflows for RNA-seq strand-specific coverage and ATAC-seq Tn5 correction

04Converts BAM alignments to normalized bigWig/bedGraph coverage tracks

05Generates publication-quality heatmaps and profile plots around genomic features

0689 GitHub stars

ユースケース

01Generating normalized genomic coverage tracks for visualization in genome browsers

02Assessing replicate consistency and sequencing depth for ChIP-seq or ATAC-seq experiments

03Comparing signal enrichment between treatment and control samples using log2 ratio analysis

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