redemux

Reprocess G4X-data with a new transcript manifest

Generates a new transcript_table.csv.gz by demultiplexing the raw feature data against a provided list of probe sequences and mapping each feature to its corresponding target gene. It then proceeds to regenerate single-cell outputs and initializes a new G4X-viewer zarr store. Does not regenerate metrics.

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Usage

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 sample.g4x, segmentation masks, panel files, images).
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 column with entries formatted as <gene>-<sequence>-<primer>. Optional gene_name or read_num columns are respected if present; otherwise they are derived from probe. 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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--no-downstream

type : flag
default : not set

Runs only the primary reprocessing step for the command and skips downstream single-cell processing and g4x-viewer.zarr generation.

Use this option when you want to inspect intermediate outputs or chain multiple processing steps before regenerating final single-cell and viewer outputs.

--branch / -b

type : string
default : command name

Selects the processed-data branch used for command output. By default, some commands i.e redemux write to a command-specific branch: <G4X-DATA>/g4x-helpers/<command>.

Use a custom branch name to write to <G4X-DATA>/g4x-helpers/<branch>. This is useful when you want to keep multiple alternative outputs, or when you want to chain commands through the same branch.

g4x-helpers redemux G4X-DATA --branch custom_process ...
g4x-helpers resegment G4X-DATA --branch custom_process ...

Set --branch _src_ to write directly into the original G4X-DATA directory.

Warning

--branch _src_ edits the source data in place and may overwrite files produced by the command.

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