What types of NGS data can deepTools handle?

deepTools is optimized for various high-throughput sequencing data types including ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq.

How does this skill assist with quality control?

It provides specialized tools to assess sequencing depth, sample correlation, PCA analysis, fragment size validation, and ChIP enrichment strength.

Can this skill help with data normalization?

Yes, it supports multiple normalization methods such as RPGC (1x coverage), CPM, RPKM, and BPM to ensure accurate comparisons between samples.

Does deepTools support file conversion for genome browsers?

Absolutely, it allows for seamless conversion from BAM alignment files to bigWig or bedGraph coverage tracks for use in tools like IGV or UCSC Genome Browser.

Is deepTools suitable for generating publication-ready figures?

Yes, it is specifically designed to create high-resolution, customizable heatmaps and profile plots that meet the standards for scientific publications.

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 visualizations and quality control metrics for genomics research.

소개

deepTools is a powerful suite of Python command-line utilities designed for the comprehensive analysis and visualization of Next-Generation Sequencing (NGS) data. It enables researchers to convert BAM alignments into normalized coverage tracks, perform rigorous quality control checks like PCA and sample correlation, and generate high-resolution heatmaps or profile plots for ChIP-seq, RNA-seq, and ATAC-seq experiments. By integrating this skill, users can automate complex bioinformatics workflows, ensure data normalization consistency, and validate experiment integrity through standardized scripts and templates.

주요 기능

Generate publication-quality heatmaps and profile plots around genomic features
Perform advanced QC including fingerprint plots, PCA, and sample correlation
81 GitHub stars
Apply diverse normalization methods like RPGC, CPM, and RPKM
Automate workflows for ChIP-seq, RNA-seq, and ATAC-seq data processing
Convert BAM alignments to normalized coverage tracks (bigWig/bedGraph)

사용 사례

Visualizing signal enrichment patterns across Transcription Start Sites (TSS) or specific genomic regions
Generating normalized bigWig files from ChIP-seq BAM files for genome browser visualization
Assessing the quality and reproducibility of biological replicates using PCA and correlation matrices

소개

주요 기능

Generate publication-quality heatmaps and profile plots around genomic features
Perform advanced QC including fingerprint plots, PCA, and sample correlation
81 GitHub stars
Apply diverse normalization methods like RPGC, CPM, and RPKM
Automate workflows for ChIP-seq, RNA-seq, and ATAC-seq data processing
Convert BAM alignments to normalized coverage tracks (bigWig/bedGraph)

사용 사례

Visualizing signal enrichment patterns across Transcription Start Sites (TSS) or specific genomic regions
Generating normalized bigWig files from ChIP-seq BAM files for genome browser visualization
Assessing the quality and reproducibility of biological replicates using PCA and correlation matrices