Tutorials¶
These tutorials walk through real PeakATail workflows from start to finish. Every command shown here was verified against the feature/product-cli branch and the full_v8_2026-05-11_152746 run directory; copy-paste should work on any machine that has the prerequisites installed.
Where to start¶
| Your situation | Start here |
|---|---|
| First time using PeakATail | Installation, then Quickstart |
| Have multiple BAM files or samples | Multi-dataset workflow |
| Want to understand a differential result biologically | Switch analysis |
| Need a single-gene visual summary | Gene track deep dive |
Tutorial map¶
01 — Installation Prerequisites, Python version, install command, and install verification.
02 — Quickstart End-to-end single-sample run in five steps: configure, run, inspect outputs, run differential, read the volcano.
03 — Multi-dataset workflow
Two BAMs in one YAML, atlas snap mode, cross-dataset cluster matching with ema switch match.
04 — Switch analysis
Full biological story: locate a significant differential row, decode every column, run ema switch length, interpret PDUI values per cluster, and conclude whether 3'UTR shortening or lengthening is happening.
05 — Gene track deep dive
Use ema switch geneview to generate a per-gene figure showing PAS positions across the gene body and per-cluster read proportions. Understand what each panel in the figure means.