Does it include effective genome sizes for standard organisms?

Yes, it contains a reference table for common assemblies including Human (GRCh38), Mouse (mm10), Zebrafish, Drosophila, and C. elegans.

Can I use this for ATAC-seq specific corrections?

Absolutely. It includes specific guidance on Tn5 offset correction using alignmentSieve and fragment size distribution analysis for ATAC-seq data.

How does deepTools handle large BAM files efficiently?

The skill suggests performance optimizations such as using multiple processors, adjusting bin sizes, and processing specific genomic regions to manage memory and speed.

Can this skill help with sample normalization?

Yes, it supports multiple normalization methods including RPGC (1x genome coverage), CPM, RPKM, and BPM, and provides guidance on which to use for different experiment types.

What sequencing types does the deepTools skill support?

The skill provides specialized workflows and best practices for ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq analysis.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: Yezez9

byYezez9

0•

数据科学与机器学习

Streamlines next-generation sequencing (NGS) data processing, quality control, and publication-quality genomic visualization.

deepTools is a comprehensive suite of Python-based utilities for high-throughput sequencing data analysis, specifically tailored for ChIP-seq, RNA-seq, and ATAC-seq workflows. This skill enables Claude to assist with complex bioinformatic tasks including BAM to bigWig conversion, sample normalization using methods like RPGC or CPM, and generating sophisticated visualizations like heatmaps and profile plots around genomic features. It provides domain-specific guidance on interpreting QC metrics, choosing effective genome sizes, and optimizing performance for large-scale genomic datasets.

主要功能

01Domain-specific analysis workflows for ChIP-seq enrichment and ATAC-seq Tn5 offset correction

02High-quality visualization generation including heatmaps and profile plots for TSS and peak regions

03Integrated file validation and workflow generators for reproducible genomic research

040 GitHub stars

05Comprehensive QC tools for sample correlation, PCA analysis, and ChIP-seq fingerprinting

06Automated BAM to BigWig conversion with integrated normalization (RPGC, CPM, RPKM, BPM)

使用场景

01Assessing ChIP-seq sample quality and replicate correlation to ensure data reliability before downstream analysis

02Creating normalized genomic coverage tracks to compare signal intensity between treatment and control samples

03Generating publication-ready heatmaps and profile plots for transcription factor binding sites and gene features

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent deeptools

For use in Claude.ai and ChatGPT