Tag: somatic mutations
-
How To Analyze Whole Genome Sequencing Data For Absolute Beginners Part 4: Visualizing and Interpreting Somatic Mutations
Introduction: From Multiple VCF Files to Biological Insights This tutorial builds upon our previous whole genome sequencing analysis pipeline, specifically the mutation calling results from Part 2A: Matched Tumor-Normal Mutation Calling with Mutect2. You should now have multiple high-confidence VCF files from different tumor-normal pairs that need to be converted to MAF (Mutation Annotation Format)
//
-
How To Analyze Whole Genome Sequencing Data For Absolute Beginners Part 2B: Unmatched Sample Mutation Calling Strategies
Introduction: Real-World Mutation Calling Challenges Welcome to Part 2B of our somatic mutation analysis series! In Part 2A, we learned the gold standard approach using matched tumor-normal pairs. However, in real-world scenarios, you often face situations where matched normal samples aren’t available. Common Unmatched Sample Scenarios Clinical Archives: Historical tumor samples without corresponding normal tissuePopulation
//
-
How To Analyze Whole Genome Sequencing Data For Absolute Beginners Part 2A: Matched Tumor-Normal Mutation Calling With Mutect2
Introduction to Matched Tumor-Normal Analysis Welcome back to our whole genome sequencing analysis journey! In Part 1, we learned how to process raw sequencing data and identify germline variants using GATK’s best practices. Now we’re ready to tackle the gold standard approach for detecting somatic mutations: matched tumor-normal analysis. What Are Somatic Mutations? Somatic mutations
//
Search
Categories
- bulk RNA-seq (27)
- chromatin accessibility (14)
- Database (4)
- Epigenetics (14)
- Genomics (10)
- HPC (5)
- 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