Differential Expression Pipeline for an RNA-Seq Drug Discovery Run
Overview
What this challenge is about.
Build a Snakemake pipeline running: fastp trimming, salmon quantification against a provided GENCODE reference, tximport for gene-level summarization, DESeq2 differential testing per treatment vs. control, and report generation. Apply standard QC checks (library size, mapping rate, PCA on rlog counts). Generate volcano plots, MA plots, and top-50 differentially-expressed-gene tables per contrast. Deliver the pipeline, the rendered Rmarkdown report, a methods section ready for inclusion in a research note, and a decisions log capturing each analytic choice (e.g. independent filtering threshold, FDR cutoff).
The Brief
What you'll do, and what you'll demonstrate.
Run a reproducible bulk-RNA-seq differential expression pipeline on a 16-sample experiment and produce a publication-quality report a senior bioinformatician will accept.
Earning criteria — what you'll demonstrate
- Orchestrate a bulk-RNA-seq analysis with a workflow manager
- Apply DESeq2 correctly including QC and contrast specification
- Communicate analytic decisions in a reviewable log
- Produce a publication-grade report on a contract-research timeline
Program Fit
Where this fits in your program.
Sharpens the same skills your degree expects you to demonstrate.
Skills
Skills you'll demonstrate.
Each one shows up on your verified credential.
Careers
Roles this prepares you for.
Real titles. Real skill bridges. Pick the one closest to your trajectory.