rna

---

raw_features.parquet

Parquet file containing raw transcript feature information pre-demultiplexing. It lists sequence, coordinates and quality scores of all detected features. This file is required for the redemux feature of G4X-helpers.

column	type	description
TXUID	str	Unique identifier for the transcript
sequence	str	Detected barcode sequence before demultiplexing
x_pixel_coordinate	float	The x-coordinate for the transcript
y_pixel_coordinate	float	The y-coordinate for the transcript
z_level	int	Z layer of identified transcript
confidence_score	float	Mean quality score for the transcript

transcript_table.csv.gz

CSV file listing all successfully demultiplexed transcript features. Includes transcript coordinates, quality score, and gene identifier. cell_id is added when transcripts are assigned to cells (will be absent after redemux with --no-downstream). The values in the cell_by_gene table are derived by applying cell segmentation masks over these transcripts.

column	type	description
TXUID	str	Unique identifier for the transcript
confidence_score	float	Mean quality score for the transcript
x_pixel_coordinate	float	The x coordinate for the transcript
y_pixel_coordinate	float	The y coordinate for the transcript
z_level	int	Z layer index of the transcript
probe_name	str	Probe identifier used for decoding
gene_id	str	Gene identifier for the decoded probe
cell_id	int	Cell the transcript is assigned to (0 = not assigned)