8 posts
A working guide to going from FASTQ files to a gene-level count matrix you trust: reference choice, STAR two-pass alignment, Salmon selective alignment, strandedness, and the QC numbers that tell you whether the run is usable.
A practical walkthrough of building a STAR index, running --quantMode GeneCounts, choosing the correct strand column in ReadsPerGene.out.tab, checking alignment quality, and converting raw counts to TPM.
A working guide to building a STAR index, running a two-pass spliced alignment of human RNA-seq, and reading the output files that tell you whether the run is any good.
A working guide to turning raw RNA sequencing reads from your own blood into quality-controlled gene and transcript quantifications, with the specific tools, flags, and reference files we would use, plus the failure modes that silently corrupt results.
A working guide to aligning and quantifying your own RNA-seq data: reference choice, STAR and Salmon parameters, strandedness, quality thresholds, and the failure modes that silently distort expression estimates.
A working GATK pipeline for calling SNPs and indels from RNA-seq reads, with filters suited to transcriptomic data and a check against genome calls.
A working guide to turning personal RNA sequencing FASTQs into gene- and transcript-level expression estimates: reference choice, selective alignment with Salmon, spliced alignment with STAR, QC thresholds, and the checks that catch a swapped or degraded sample.
A practical guide to picking a human genome build and annotation for RNA-seq, building STAR and salmon indexes correctly, and checking that the reference you built is the one your quantification assumes.