tile-xenium

Take transcripts.csv from Xenium and split it into smaller parts, so that I can be used more easily with Baysor. In addition, this decodes the 10x cell ids to integer numbers.

For Baysor, the most relevant Xenium output file is transcripts.csv.gz. The file format is documented online here. Here are a few quick notes about some of its columns:

• cell_id: If a transcript is NOT associated with a cell, it will get -1. If it is associated with a cell, this column will have a positive integer cell ID.
• x_location, y_location, z_location: These three columns store the (x, y, z) coordinates of the transcript in microns. The origin is found in the upper-left corner of the bottom z-slice, as the following image illustrates.
• feature_name: The gene associated with the transcript.
• qv: Phred-scaled quality score of all decoded transcripts. It is up to the customer to determine a suitable Q-Score threshold when analyzing Xenium data. At 10x Genomics, we typically filter out transcripts with Q-Score < 20.

To preprocess Xenium’s transcript CSV file for Baysor, the script will perform the following steps:

• Filter out negative control transcripts.
• Filter out transcripts whose Q-Score falls below a specified threshold (default: 20).
• Baysor required that the cell_id is an integer. UNASSIGNED cells will be substituted with 0 and the encoded cell id will be reversed to an integer. The conversion is described here.

Usage

Create tiles, filter transcripts from transcripts.csv based on Q-Score threshold. Remove negative controls

Usage: tile-xenium [OPTIONS] <IN_FILE>

Arguments:
  <IN_FILE>  The path to the transcripts.csv or .parquet file produced by Xenium

Options:
      --min-qv <MIN_QV>
          The minimum Q-Score to pass filtering [default: 20]
      --width <WIDTH>
          The width of the tiles [default: 4000]
      --height <HEIGHT>
          The height of the tiles [default: 4000]
      --overlap <OVERLAP>
          Overlap betweent the tiles [default: 500]
      --minimal-transcripts <MINIMAL_TRANSCRIPTS>
          Minimal number of transcripts per tile. If number is less, 
          the tile will be expanded by overlap in all directions [default: 100000]
      --nucleus-only
          Only keep transcripts that are in the nucelus. All other transcripts will
          not be assigned to a cell
      --exclude-genes [<EXCLUDE_GENES>...]
          Exclude genes If a gene starts with any of these values, it will be removed
          [default: NegControlProbe_ antisense_ NegControlCodeword_ BLANK_ UnassignedCodeword_]
      --out-dir <OUT_DIR>
          Path for outout file. The output file will be names after the following schema:  
            X{x-min}-{x-max}_Y{y-min}-{y-max}_filtered_transcripts_nucleus_only_{nucleus_only}.csv  
            E.g.: X0-24000_Y0-24000_filtered_transcripts_nucleus_only_false.csv [default: .]
  -h, --help
          Print help
  -V, --version
          Print version