-
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…
//
-
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…
//
-
HPC Data Management for NGS Analysis: Storage, Transfer, and Sharing Best Practices
Video Tutorial Introduction to Data Management on High-Performance Computing Systems High-Performance Computing (HPC) systems have become essential tools for Next-Generation Sequencing (NGS) data analysis. These powerful computing environments allow researchers to process and analyze massive genomic datasets that would be impossible to handle on standard desktop computers. However, working effectively with HPC systems requires understanding…
//
-
High Performance Computing (HPC) Job Submission Systems: A Beginner’s Guide to Slurm
Video Tutorial Introduction: Understanding High Performance Computing Have you ever tried to run a program on your computer, only to find that it takes hours or even days to complete? Or perhaps you needed to analyze a huge dataset that wouldn’t even fit in your computer’s memory? These are the kinds of problems that High…
//
-
How to Analyze RNAseq Data for Absolute Beginners 21: A Comprehensive Guide to Batch Effects & Covariates Adjustment
Video Tutorial Introduction to Batch Effects in RNA-seq Analysis In high-throughput sequencing experiments, batch effects represent one of the most challenging technical hurdles researchers face. These systematic variations arise not from biological differences between samples but from technical factors in the experimental process. Understanding and properly adjusting for batch effects is essential for generating reliable…
//
-
How to Analyze RNAseq Data for Absolute Beginners Part 20: Comparing limma, DESeq2, and edgeR in Differential Expression Analysis
Video Tutorial Introduction Differential expression (DE) analysis represents a fundamental step in understanding how genes respond to different biological conditions. When we perform RNA sequencing, we’re essentially taking a snapshot of all the genes that are active (or expressed) in our samples at a given moment. However, the real biological insights come from understanding how…
//
-
How to Analyze RNAseq Data for Absolute Beginners Part 19: Understanding RNA-Seq Gene Expression Normalization
Video Tutorial Introduction: Why Normalization Matters in RNA-Seq Analysis RNA sequencing (RNA-seq) has revolutionized our ability to measure gene expression, but the raw data needs careful processing to yield meaningful biological insights. In this comprehensive guide, we’ll explore why normalization is crucial and how to convert between different expression metrics using R. Building on our…
//
-
How to Analyze RNAseq Data for Absolute Beginners Part 18: Analyzing Viral Gene Expression in Host RNA-seq Data
Understanding viral gene expression patterns during infection is crucial for studying host-pathogen interactions. This comprehensive guide will walk you through the process of accurately quantifying viral transcripts from RNA-seq data of infected host cells, providing you with practical approaches for this challenging analysis. Video Tutorial The Challenge of Viral RNA-seq Analysis When we sequence RNA…
//
-
How to Analyze RNAseq Data for Absolute Beginners Part 17: Viral Sequence Detection
Video Tutorial Introduction to Viral Sequence Detection The intersection of high-throughput sequencing and viral genomics has transformed our understanding of viral biology and disease. Through RNA-seq and whole-genome sequencing (WGS), researchers can now peer into the complex relationship between viruses and their hosts with unprecedented clarity. This technological breakthrough has revolutionized both biomedical research and…
//
-
How to Analyze RNAseq Data for Absolute Beginners Part 16: A Comprehensive Tutorial on Identifying Fusion Genes
Video Tutorial Understanding Fusion Genes: Key Concepts for Cancer Research What Are Fusion Genes and Why Do They Matter? Fusion genes represent a fascinating phenomenon in cancer biology where two previously separate genes join together, often creating proteins with altered or entirely new functions. These genetic mergers typically arise through chromosomal rearrangements like translocations, deletions,…
//
Search
Subscribe
Never miss the latest tutorials from NGS Learning Hub
Categories
- bulk RNA-seq (20)
- chromatin accessibility (10)
- Database (2)
- Epigenetics (10)
- HPC (3)
- Metagenomics (1)
- Scientific Programming (3)
- Transcriptomics (21)
Recent Posts
- Build Once, Run Anywhere: Creating Portable NGS Analysis Environments with Docker
- 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
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