catcheR_10XcatchQC - Fine-Tune iPS2-10X-seq Perturbation Assignment

Optionally, uou can refine shRNA assignment thresholds without re-running the full catcheR_10Xcatch analysis using:

  • catcheR_10XcatchQC: regenerate QC plots with alternative thresholds or thresholding mode (e.g. switch from bimodal to noise)

  • catcheR_filtercatch: re-apply filters using chosen thresholds

These tools only rerun the second half of the pipeline, saving time and computing resources.

Step-by-step

  1. In the same working folder used previously with catcheR_10Xcatch, run catcheR_10XcatchQC. This will regenerate QC plots and suggest new thresholds.

catcheR_10XcatchQC(
    group = c("docker", "sudo"),
    folder = "path/to/working/folder",
    reference = "GGCGCGTTCATCTGGGGGAGCCG",
    mode = "bimodal",
    sample = 1,
    x = 100,
    y = 400
)

Arguments:

  • group: “docker” or “sudo” depending on your system permissions

  • folder: working directory

  • reference: reverse complement of constant region before the UCI (default: GGCGCGTTCATCTGGGGGAGCCG)

  • mode: thresholding strategy, either: - "bimodal": uses the valley in the UMIxUCI distribution (default) - "noise": 1.35 × number of UCIs with 1 UMI

  • sample: sample number (default = 1)

  • x / y: crop limits for the x and y axes of UMIxUCI plots (defaults: 100, 400)

Example:

catcheR_10XcatchQC(
    group = "docker",
    folder = "path/to/working/folder",
    mode = "noise"
)

Note

This function should be run once per sample (sample = 1, sample = 2, etc.)

The arguments and outputs are identical to those in catcheR_10Xcatch, but this step focuses only on quality control plot generation and threshold estimation.