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.

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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

Arguments / Options

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G4X-DATA

type : directory
example : path/to/g4x_output

Positional path to a G4X sample output directory.
The folder must follow the expected schema (e.g., contain run_meta.json, segmentation masks, panel files, single-cell outputs).
Provide this argument directly after the specified command, i.e:
g4x-helpers COMMAND G4X-DATA

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--manifest

type : file path
example : path/to/transcript_panel.csv

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.

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--batch-size

type : integer
default : 1.000.000

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

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--in-place

type : flag
default : not set

By default, commands write their outputs to <G4X-DATA>/g4x_helpers/<command>, leaving the original data untouched. Using --in-place instead writes outputs directly into the specified G4X-DATA directory, which may be required when chaining certain commands.

Note: this will override any existing artifacts modified by the command.
Please refer to each feature’s documentation to see which files may be updated.

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