4 posts
A step-by-step bioinformatics workflow for taking bulk RNA sequencing FASTQs from your own blood sample through quantification, quality control, normalization, and interpretation, with the tools, flags, and failure modes named.
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 practical pipeline for turning your own bulk RNA-seq FASTQs into quantified gene and transcript expression, with the tool choices, flags, QC thresholds, and failure modes that matter for a single-person longitudinal dataset.
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.