Tag: peak calling
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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 1: From FASTQ To Peaks With HOMER
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 data analysis…
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Recent Posts
- How To Analyze ATAC-seq Data For Absolute Beginners Part 1: From FASTQ To Peaks
- How To Analyze ChIP-seq Data For Absolute Beginners Part 5: Mastering Reproducibility With IDR Analysis
- How To Analyze ChIP-seq Data For Absolute Beginners Part 4: From FASTQ To Peaks With MACS2
- How To Analyze ChIP-seq Data For Absolute Beginners Part 3: Differential Binding Analysis and Motif Discovery
Tags
Alternative Splicing Analysis batch effects ChIP-seq ComBat-seq Counts covariates adjustment CPM Data Sharing DESeq2 Differential Expression edgeR FPKM gene expression HOMER HPC Isoform limma MACS2 miRNA miRNA-seq mixed linear models Normalization peak calling Quantification Salmon TPM Transcript Virus Virus-Host Virus Gene Expression