Pipeline overview

The pipeline has three user-facing phases: Samples, Run, and Results. A run records the selected samples, comparisons, parameters, tool versions, and outputs so the same decision can be reproduced later.

FASTQ data → Samples and groups → Run configuration → QC → cleanup → quantification → DESeq2 → optional pathways → Results

Samples: define the experiment

Attach datasets, inspect read layout, and create groups. Groups represent biological conditions; they are not merely file folders. The baseline group determines the direction of every comparison.

Run: make analysis decisions

Choose comparisons, cleanup intensity, quantification method, and optional pathway analyses. Review the final configuration before launch. After launch, the run’s inputs and configuration form its reproducibility record.

Results: interpret and export

The Results area combines significant genes, expression plots, sample-quality views, pathway summaries, configuration, and downloads. Start with quality and preprocessing impact before interpreting biological differences.

Continue with Samples and groups, Configure a run, or Results overview.