Command Line Interface
Chr3D provides a comprehensive command-line interface for all pipelines.
chr3d [COMMAND] [OPTIONS]Commands Overview
| Command | Description |
|---|---|
| chr3d bulk-hic | Bulk Hi-C pipeline (single sample) |
| chr3d sn-hic | Single-nucleus Hi-C pipeline (multiple cells) |
| chr3d chia-pet | ChIA-PET pipeline (linker filter → map → peaks → loops) |
| chr3d hichip | HiChIP pipeline (align → dedup → MboI purify → background) |
| chr3d digest | Generate restriction fragment BED from genome FASTA |
Global Options
These options are available for all commands:
| Option | Description |
|---|---|
-v, --verbose | Enable DEBUG-level logging |
--log-file FILE | Write log to FILE in addition to stdout |
-h, --help | Show help message and exit |
Environment Variables
| Variable | Description |
|---|---|
CHR3D_THREADS | Default thread count (overridden by --threads) |
CHR3D_TMPDIR | Temporary directory for intermediate files |
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