Concepts

These pages explain what is happening inside PeakATail before you run it. Read them when you want to understand why the pipeline is structured the way it is, not just how to invoke it.

Before you run — conceptual map

Question	Where to look
How does data move from BAM to clusters.h5ad?	Data flow
What is every file in my output directory?	Output files
What is APA and why does it matter in single-cell data?	Single-cell APA primer

Page descriptions

Data flow A Mermaid diagram of every pipeline stage with the file types that flow between them. Covers both the single-sample path (one BAM) and the multi-sample path (two or more BAMs with atlas snap or coordinate merge).

Output files A reference entry for every file PeakATail writes. Includes the canonical path, format, and the pipeline stage that produces it. Useful when you want to load a specific artifact into Python or pass it to another tool.

Single-cell APA primer A ~600-word explanation of alternative polyadenylation for a reader who knows single-cell sequencing but has not worked with 3' end biology before. Covers what a PAS is, why 3'UTR length is regulated per cell type, and how PDUI quantifies it.