REPRODUCIBLE RNA-SEQ QC

RNA-seq QC report template

A concise structure for QC handoff, review and auditability

A report is useful when another qualified reviewer can understand what was checked, why a sample was flagged and what should happen next.

1. Run context

Record the project or run identifier, assay, organism, library preparation, read layout, sequencing platform, date and reviewer. State which files and MultiQC version were used.

2. QC source and rule profile

Link the original MultiQC report and structured export. List the metrics available and the profile used for PASS, WARN and FAIL decisions. Thresholds should be described as protocol-specific starting points, not universal scientific standards.

3. Sample-level decision table

For each sample, include: sample identifier; status; relevant observed metric; comparison or boundary; concise reason; and next action. Keep the table short enough to use during a project review meeting.

4. Cohort observations

Summarize shared patterns such as a lane-level change, broad GC shift, consistent trimming loss or a group of samples with lower depth. Separate observations from conclusions that require experimental context.

5. Decisions and exceptions

State which samples can proceed, which require a follow-up check and which should pause. If a reviewer accepts an exception, document the reason, decision-maker and any downstream limitation.

6. Export and sign-off

Save both a human-readable PDF and a structured export alongside the original QC artifacts. Record the tool version and date so the decision can be repeated later.

Generate a starting report locally

Use the free GenomQC browser report to create a structured review queue from supported MultiQC exports. Processing is local to the browser; the selected QC file is not uploaded to a GenomQC server.

Read the RNA-seq QC checklist or learn how to interpret MultiQC for RNA-seq.

Scope

GenomQC is a research-use QC prioritization tool. It does not replace protocol knowledge, laboratory SOPs or qualified scientific review.