catcheR_sortcatch - Barcode reassignment

catcheR_sortcatch is an optional function that corrects the annotated cell-by-gene count matrix obtained with catcheR_10Xcatch or catcheR_scicatch. It reassigns the perturbation of any cell belonging to an hPSC clone with reliable evidence of a shRNA-barcode swap, based on the results of catcheR_step1QC.

Steps

1. In a new working folder:

   1. Copy the annotated count matrix (e.g., silencing_matrix.csv)

   2. Copy the CSV file with the list of UCI-BCs with reliable evidence of a shRNA-barcode swap (e.g., reliable_clones_swaps.csv; output of catcheR_step1QC)

2. Run catcheR_sortcatch:

   catcheR_sortcatch(
       group = c("sudo", "docker"),
       folder,
       expression.matrix,
       swaps
   )
   

   Example usage:

   catcheR_sortcatch(
       group = "docker",
       folder = "path/to/working/folder",
       expression.matrix = "silencing_matrix.csv",
       swaps = "reliable_clones_swaps.csv"
   )
   

Arguments

• group: string with two options: sudo or docker, depending on the user group (info)

• folder: string with the working folder path

• expression.matrix: string with the filename of the annotated count matrix CSV

• swaps: string with the filename of the swap list CSV file

Output

catcheR_sortcatch outputs an updated annotated gene expression matrix CSV file called silencing_matrix_updated.csv, in which the “BC” and “GENE” annotations have been corrected to reflect the actual shRNA encoded in each cell.