Tag: VCF
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How To Analyze Whole Genome Sequencing Data For Absolute Beginners Part 3: Annotating SNVs and Mutations with Multiple Tools
A comprehensive step-by-step guide to understanding the functional impact of genomic variants using GATK Funcotator, Ensembl VEP, SnpEff, and ANNOVAR Introduction: From Variants to Biological Meaning After successfully identifying genomic variants using GATK (covered in Part 1) and discovering somatic mutations with Mutect2 (detailed in Part 2A), you now have VCF files containing thousands of
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The Complete Guide to NGS Data Types and Formats: From Raw Reads to Analysis-Ready Files
Master the essential file formats in next-generation sequencing analysis Introduction: Understanding the NGS Data Ecosystem Next-generation sequencing (NGS) has revolutionized biological research by enabling us to read DNA, RNA, and epigenetic modifications at an unprecedented scale. However, with this power comes complexity – NGS workflows generate dozens of different file formats, each serving specific purposes
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Categories
- bulk RNA-seq (27)
- chromatin accessibility (14)
- Database (4)
- Epigenetics (14)
- Genomics (10)
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- Metagenomics (1)
- Quick Tips (1)
- RNA-seq (14)
- Scientific Programming (5)
- Single Cell Sequencing (14)
- Transcriptomics (28)
Recent Posts
- How to Analyze Single-Cell RNA-seq Data – Complete Beginner’s Guide Part 12: Build Gene Co-expression Networks Using hdWGCNA
- How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 11: Copy Number Variation Analysis Using CopyKAT
- No More Command-Line Only: Run Jupyter Lab, RStudio, and VS Code Interactively in Your Browser on Any HPC Cluster with Pixi
- How to Analyze Single-Cell RNA-seq Data – Complete Beginner’s Guide Part 10: Cell-Cell Communication Analysis Using NicheNet
Tags
Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility CNV DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression heatmap HOMER HPC Isoform limma MACS2 MAF miRNA miRNA-seq MSigDB Normalization peak calling RNA-seq SLURM somatic mutations Transcript VCF whole genome sequencing