Troubleshooting¶

I cannot open C-Studio¶

Download the package for your platform from the official GitHub Releases page. On macOS, verify the download source, then Control-click the app and choose Open. On Windows, verify the source before continuing through a SmartScreen warning.

C-Studio cannot find my project files¶

Select a folder containing regular files at its top level. Supported files are .agp, .gfa/.gfa1, .paf, .depth/.bedgraph/.bg, .cool, and .mcool; text files may end in .gz. Grant C-Studio access to the selected folder if macOS or Windows asks for permission.

The heatmap or an evidence view is empty¶

AGP component IDs must match the chromosome or segment names in the contact map, PAF, coverage, and GFA files. Then check the current view, resolution, colour range, normalisation, and layer visibility. Returning to the full assembly view and using Auto colour range is a safe reset.

I cannot save or restore history¶

Use Save As once to choose a writable, uncompressed AGP destination. Auto-save cannot overwrite an .agp.gz input. To restore history, keep <AGP-prefix>.history.json next to the matching AGP; C-Studio ignores a malformed or incompatible sidecar but still opens the AGP.

The GFA view or homolog layout is missing¶

The GFA needs valid S records with matching segment names. For homolog layout, set Homolog regex so capture group 1 is the group and capture group 2 is its member order; for example, (Chr\d+)g(\d+) matches Chr01g1.

“Load example project” does not work¶

This helper requires the source checkout's examples/ directory. In a packaged application, load the example files individually instead.