Tag: FASTQ
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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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How to Analyze RNAseq Data for Absolute Beginners Part 2: From Fastq to Counts – Best Practices
Introduction The most straightforward way to obtain a count table is to request it directly from your sequencing company or your institution’s sequencing core. This option may involve an additional fee. However, for those eager to learn or save money, let’s walk through the process together. Before we dive in, a quick reminder: If you…
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- ATAC-seq (7)
- bulk RNA-seq (27)
- chromatin accessibility (14)
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- RNA-seq (20)
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- Single Cell Sequencing (27)
- Transcriptomics (28)
Recent Posts
- Bioinformatics Isn’t Dead. The Pipeline-Runner Is.
- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 7: Genome-Wide Differential TF Activity with chromVAR and limma
- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 6: Footprinting Analysis
- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 5: Differential Accessibility Analysis
Tags
Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression GSE282769 heatmap HOMER HPC Isoform limma MACS2 miRNA miRNA-seq MSigDB Normalization peak calling Pixi bioinformatics environment RNA-seq single-cell epigenomics beginners guide SLURM somatic mutations Transcript whole genome sequencing