redemux

Reprocess G4X-output with a new transcript manifest

Replaces or updates the transcript manifest in a G4X run, reassigns transcripts via demultiplexing, and regenerates all downstream single-cell data and .tar viewer files.

Usage

Note

Global options --threads/-t & --verbose/-v must be supplied on the main entrypoint before the subcommand:

g4x-helpers --threads 16 -v 2 COMMAND /path/to/g4x_data [OPTIONS]

use g4x-helpers --help for more information

argument descriptions

---

required

G4X-DATA (argument)

Positional path to a G4X sample output directory.
The folder must follow the expected schema (e.g., run_meta.json, segmentation masks, panel files, single-cell outputs).
Provide this argument after command-specific options.

--manifest: (type: str)

Path to the new transcript manifest for demuxing.
Must contain a probe_name column with entries formatted as <gene>-<sequence>-<primer>. Optional gene_name or read columns are respected if present; otherwise they are derived from probe_name. Invalid probe names are ignored.

optional

--batch-size: (type: int default: 1,000,000)

Number of transcripts to process per batch during demultiplexing.
Larger batch sizes may improve performance but increase memory usage.

--in-place: (flag default: False)

By default, outputs are written to <G4X-DATA>/g4x_helpers/<command>, leaving the source data untouched.
Add --in-place to write results directly into the provided G4X-DATA folder (overwriting existing artifacts for that command).

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