Category: chromatin accessibility
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How To Analyze CUT&RUN/Tag Data For Absolute Beginners: From FASTQ to Peaks
A comprehensive step-by-step guide to understanding and analyzing CUT&RUN and CUT&Tag data for high-precision chromatin profiling Introduction: The Evolution of Chromatin Profiling Technologies Understanding protein-DNA interactions and chromatin organization remains one of molecular biology’s most fundamental challenges. While ChIP-seq and ATAC-seq have been the gold standards for chromatin profiling, CUT&RUN (Cleavage Under Targets and Release…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 4: ATAC-seq and RNA-seq Integration
Introduction: The Power of Multi-omics Integration Modern genomics research has evolved beyond studying isolated molecular mechanisms. To truly understand complex biological processes and disease mechanisms, researchers need to examine multiple layers of genomic information simultaneously. This tutorial introduces beginners to the powerful approach of integrating ATAC-seq and RNA-seq data using R, enabling a more comprehensive…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 3: Footprinting Analysis
Introduction: Unveiling Transcription Factor Binding Sites with ATAC-seq Footprinting After mastering the basics of ATAC-seq data processing and peak calling in our previous tutorials, we now delve into one of the most powerful analytical techniques this assay enables: footprinting analysis. While standard ATAC-seq analysis reveals regions of open chromatin, footprinting takes this a step further…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 2: Differential Binding Analysis Using DiffBind
Introduction: The Power of Comparative ATAC-seq Analysis ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) has revolutionized chromatin accessibility mapping by requiring minimal input material and offering streamlined workflows. While identifying accessible regions in a single condition provides valuable insights, the most compelling biological discoveries often come from comparing accessibility between different experimental conditions –…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 1: From FASTQ To Peaks
Introduction: Understanding ATAC-seq At the heart of molecular biology lies a fundamental question: how do cells regulate which genes are expressed and when? One powerful technique to explore this question is Assay for Transposase-Accessible Chromatin sequencing, commonly known as ATAC-seq. This tutorial introduces beginners to the fascinating world of ATAC-seq data analysis using HOMER and…
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How To Analyze ChIP-seq Data For Absolute Beginners Part 5: Mastering Reproducibility With IDR Analysis
Introduction: Why Reproducibility Is Crucial In ChIP-seq Analysis Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has revolutionized our understanding of protein-DNA interactions across the genome. However, like all experimental techniques, ChIP-seq is subject to both technical and biological variability. This variability creates a fundamental challenge: how do we distinguish genuine protein binding events from experimental…
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How To Analyze ChIP-seq Data For Absolute Beginners Part 4: From FASTQ To Peaks With MACS2
Introduction: Expanding Your ChIP-seq Analysis Toolkit Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has revolutionized our understanding of protein-DNA interactions across the genome. In this fourth installment of our ChIP-seq tutorial series, we explore an alternative approach to peak calling using MACS2 (Model-based Analysis of ChIP-Seq), a widely used and statistically robust tool that complements the…
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How To Analyze ChIP-seq Data For Absolute Beginners Part 3: Differential Binding Analysis and Motif Discovery
Introduction: Moving Beyond Basic Peak Calling In our previous tutorials, we walked through the fundamental process of ChIP-seq analysis, from raw sequencing reads to identifying where a protein of interest binds to DNA. While finding these binding sites (peaks) is a crucial first step, it’s often just the beginning of extracting meaningful biological insights from…
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How To Analyze ChIP-seq Data For Absolute Beginners Part 2: Visualizing ChIP-seq Data
Video Tutorial Introduction: Why Visualization Is Critical In ChIP-seq Analysis After processing raw ChIP-seq data and identifying protein-DNA binding sites in Part 1, visualization becomes the crucial next step that transforms abstract numerical data into interpretable biological insights. While peak calling identifies where proteins bind to DNA, visualization helps answer questions about how and why…
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How To Analyze ChIP-seq Data For Absolute Beginners Part 1: From FASTQ To Peaks With HOMER
Video Tutorial Introduction: Understanding ChIP-seq At the heart of molecular biology lies a fundamental question: how do cells regulate which genes are expressed and when? One of the most powerful techniques to explore this question is Chromatin Immunoprecipitation followed by sequencing, commonly known as ChIP-seq. This tutorial introduces beginners to the fascinating world of ChIP-seq…
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Categories
- bulk RNA-seq (20)
- chromatin accessibility (10)
- Database (2)
- Epigenetics (10)
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- Metagenomics (1)
- Scientific Programming (2)
- Transcriptomics (21)
Recent Posts
- The Complete Guide to NGS Data Types and Formats: From Raw Reads to Analysis-Ready Files
- How To Analyze CUT&RUN/Tag Data For Absolute Beginners: From FASTQ to Peaks
- How To Analyze ATAC-seq Data For Absolute Beginners Part 4: ATAC-seq and RNA-seq Integration
- How To Analyze ATAC-seq Data For Absolute Beginners Part 3: Footprinting Analysis
Tags
Adapter Trimming Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility Conda Environment Setting Count DESeq2 Differential Expression edgeR FASTQ gene expression Gene Expression Quantification HOMER HPC Isoform limma MACS2 miRNA miRNA-seq Normalization PCA peak calling R Reads Mapping RNAseq analysis RNAseq analysis for beginners RStudio Transcript