Get started¶

This walkthrough keeps the source AGP recoverable and makes the boundary between evidence and edits explicit.

If the input files have not been generated yet, follow Prepare input files first.

Download the example data¶

Download examples.tar.gz from the C-Studio v0.5.0 release, then extract the archive. To open an extracted example, choose Add Data → Load project folder… and select its project directory.

The archive contains these example files:

groups.final.agp
alfalfa.mapq1.mcool
alfalfa.coverage.bedgraph
ref.align.paf
alfalfa.p_utg.noseq.gfa

1. Prepare a project directory¶

For a real project, place copies of the inputs in one dedicated directory. An AGP is required for assembly editing. Other evidence is optional.

my-project/
├── assembly.agp
├── contacts.mcool
├── alignments.paf
├── coverage.bedgraph
└── assembly.gfa

2. Load data¶

Choose Add Data → Load project folder…. Alternatively, use the individual entries below Add Data.

When running from a source checkout, Load example project can open the checkout's local examples/ directory. In a packaged application, download and extract the v0.5.0 example archive as described above, then load an example project directory manually.

3. Check the workspace¶

Confirm the status bar and Project Info show the expected assembly and matrix. Then inspect:

• the main heatmap and coverage track;
• the Overview, Synteny, and GFA inspector tabs;
• the chromosome, block, and contig annotation boxes;
• the homolog regular expression when a GFA is present.

If contig identifiers do not match across AGP, contact-map bins, PAF, coverage, and GFA, the corresponding evidence cannot be projected reliably.

4. Navigate and select¶

• Drag the heatmap to pan.
• Scroll to pan diagonally; use the platform-specific modified scroll gestures for resolution switching or vertical movement.
• Use Fit to return to the whole assembly.
• Enter contig or contig:start-end in the X/Y Jump fields.
• Shift-click an assembly overlay to select a contig or chromosome. Shift-drag selects several contigs; Command/Control-click in synchronized tracks toggles individual contigs.

See navigation and selection for the full interaction model.

5. Make one reversible edit¶

Right-click the selected assembly item and choose an operation such as Reverse / rotate selection, Copy, or Move to debris. Watch the contact map, tracks, and evidence views reproject to the edited AGP layout.

Use Undo or the History list to verify reversibility before continuing. Deletion requires confirmation and reports whether any source interval will have no copies left.

6. Save an edited AGP¶

Press Cmd+S on macOS or Ctrl+S on Windows, or click the save icon. C-Studio saves the edited AGP and a same-prefix .history.json sidecar that contains the compatible undo/redo timeline.

Compressed .agp.gz input is never overwritten directly. Save to a plain AGP target before enabling auto-save.