Tagged: tutorial
35 posts found
How to Read a FastQC Report: Warnings, Failures, and Fixes
A senior bioinformatician walks through the FastQC sections that real beginners miss, with screenshots and decisions to make at each step.
STAR vs Salmon vs HISAT2: A Hands-On Benchmark
A hands-on RNA-seq aligner benchmark: working STAR, Salmon, and HISAT2 commands, real runtime and memory numbers, and how much the DEG list actually changes.
Salmon From FASTQ to Counts: A Complete Tutorial
A complete Salmon tutorial with decoy-aware indexing, quantification flags explained, tximport into R, DESeq2 integration, and QC checks at every step.
PyDESeq2 vs DESeq2 in R: Validation and Scanpy Workflow
Does PyDESeq2 really match R DESeq2? A tutorial on validating results against R, running PCA with scanpy and AnnData, and exporting DEGs for enrichment.
Publication-Ready RNA-Seq Plots in R with ggplot2
Reviewer-ready RNA-seq plots in R: volcano with gene labels, z-score heatmap with annotation bars, PCA with variance explained, and journal export settings.
ORA vs GSEA in R: clusterProfiler Pathway Analysis Tutorial
ORA and GSEA answer different questions. A working clusterProfiler tutorial with FDR correction, proper backgrounds, and side-by-side result interpretation.
GTF vs GFF3 Files: Format Differences and RNA-Seq Fixes
GTF and GFF files from the same database often disagree, prokaryotic files lack exon features, AGAT fixes some and breaks others. A practical field guide.
Nextflow RNA-Seq Tutorial: Build Your First Pipeline
A minimal Nextflow DSL2 RNA-seq pipeline in under 80 lines: three processes, channel wiring, Docker config, and how to read the execution report and DAG output.
Reducing GO Term Redundancy: simplify, rrvgo, and What Works
After enrichment you get hundreds of overlapping GO terms. A tutorial on clusterProfiler simplify, rrvgo, REVIGO, and a custom uniqueness-score fallback.
Pathway Enrichment Analysis: GSEA and ORA in R and Python
Pathway enrichment end to end: GSEA and ORA in R with clusterProfiler and fgsea, plus the Python equivalent with gseapy, across MSigDB, KEGG, and GO sets.
fastp vs Trimmomatic vs BBDuk: A Benchmark on RNA-Seq Reads
A side-by-side benchmark of fastp, Trimmomatic, and BBDuk on paired-end RNA-seq data: speed, post-trim quality, mapping rate, and downstream DEG impact.
DESeq2 Tutorial in R: Count Matrix to Volcano Plot
A complete DESeq2 tutorial in R: loading counts, building the design formula, running DE, applying lfcShrink, generating a volcano plot, and exporting results.
DESeq2 Contrasts: Multiple Conditions and Multi-Factor Designs
Three conditions, paired designs, two-factor experiments, and time courses: how to build the design formula, specify contrasts, and avoid common mistakes.
RNA-Seq Plots: Volcano, MA, and Heatmap in R and Python
Publication-ready RNA-seq plots in R and Python: volcano with ggplot2/ggrepel, MA plots, and DEG heatmaps with pheatmap and seaborn, plus 300 dpi export.
Bulk RNA-Seq Deconvolution: CIBERSORTx and MuSiC Tutorial
Estimate cell type proportions from bulk RNA-seq using CIBERSORTx and MuSiC. Reference selection, batch correction, validation, and result interpretation.
RNA-Seq Batch Correction: ComBat-Seq vs RUVSeq vs sva
How to choose a batch-effect correction tool: ComBat-Seq, RUVSeq, and sva compared, including unknown batch sources and reporting it in your methods.
Salmon to Differential Expression in Python with PyDESeq2
A pipeline-focused PyDESeq2 tutorial: load Salmon quant.sf into a count matrix, fit a DeseqDataSet, run Wald tests, apply apeGLM shrinkage, export DEGs. No R.
How to Run DESeq2 in R from Salmon quant.sf Files
DESeq2 in R from Salmon counts: import quant.sf with tximeta, build a DESeqDataSet, run the Wald test, apply apeglm shrinkage, and export a ranked DEG table.
How to Build a DESeq2 Count Matrix in Python
Python tutorial: parse featureCounts output, aggregate Salmon quant.sf, build a tx2gene map, and save a DESeq2-ready integer count matrix with pandas.
STAR RNA-Seq Alignment Tutorial: FASTQ to Gene Counts
Complete STAR tutorial: download genome and GTF, build an index with the right sjdbOverhang, run paired-end alignment, and load GeneCounts into R for DESeq2.
How to Build a Decoy-Aware Salmon Index for RNA-Seq
Step-by-step Salmon tutorial: download GENCODE references, build a decoy-aware index, run salmon quant with gcBias and seqBias, and verify mapping rates.
FASTQ Quality Control: FastQC, fastp, and MultiQC Workflow
Bulk RNA-seq QC end to end: run FastQC on raw reads, trim adapters with fastp, rerun QC, and aggregate everything into one MultiQC report, with parallel runs.
How to Download RNA-Seq FASTQ Data from GEO and SRA
Download bulk RNA-seq FASTQ files from GEO and SRA: prefetch, fasterq-dump, pysradb metadata, batch downloads, and fixes for the most common errors.
Volcano and MA Plots in R: DESeq2 and ggplot2 Tutorial
Publication-quality volcano and MA plots from DESeq2 results in R: ggplot2 from scratch, ggrepel gene labels, EnhancedVolcano, and how to read them.
RNA-Seq PCA and Sample Clustering in Python: QC Tutorial
Python tutorial: normalize RNA-seq counts, run PCA with scikit-learn, build a sample distance heatmap, and spot outliers before differential expression.
PyDESeq2 Tutorial: Differential Expression Analysis in Python
The complete PyDESeq2 reference in Python: DeseqDataSet, DeseqStats, apeglm shrinkage, multi-factor designs, multiple contrasts, and pandas result filtering.
DESeq2 Tutorial in R: From Count Matrix to Results
Step-by-step DESeq2 in R: build a DESeqDataSet, understand size factors and dispersion, run DESeq(), interpret the results columns, then shrink and filter DEGs.
Set Up an RNA-Seq Conda Environment on Ubuntu or macOS
Install Miniforge, conda, bioconda, R 4.4, and DESeq2 for bulk RNA-seq: reproducible environments, version pinning, and fixes for common install errors.
Salmon quant.sf Explained: Mapping Rates and DESeq2 Import
Understand Salmon quant.sf columns, mapping rates, effective length, NumReads, TPM, and the correct handoff to tximport, tximeta, and DESeq2.
tximport vs tximeta: Import Salmon quant.sf into DESeq2
Import Salmon quant.sf into R with tximeta and tximport: build a tx2gene table, fix ID-mismatch errors, and set up a DESeqDataSet for multi-factor designs.
STAR vs HISAT2 vs Salmon: Which Aligner Should You Use?
STAR aligns to the genome, HISAT2 uses less memory, Salmon skips alignment. What each approach means for your RNA-seq results and when each is the right call.
RNA-Seq Sample Preparation: RNA Extraction to FASTQ Files
RNA-seq sample preparation from RNA extraction and quality checks through library preparation, Illumina sequencing, base calling, and FASTQ files.
fastp vs Trimmomatic: RNA-Seq Adapter Trimming Tutorial
When adapter trimming helps, when it hurts, and how to run Trimmomatic and fastp on RNA-seq data with the parameter choices that actually matter.
How to Run FastQC and MultiQC on Multiple FASTQ Files
A hands-on guide to automating RNA-seq QC across dozens of samples using FastQC and MultiQC, with bash and Python scripts for parsing and flagging failures.
Bulk RNA-Seq Pipeline: FASTQ to Gene Counts Step by Step
Every computational step in bulk RNA-seq, explained: from FASTQ quality control through trimming, alignment, and quantification to your final count matrix.