scReadSim.Utility.scRNA_bam2countmat_paral_MultiSample

scReadSim.Utility.scRNA_bam2countmat_paral_MultiSample(cells_barcode_file, INPUT_bamfile, outdirectory, n_cores=1, UMI_modeling=True, UMI_tag='UB:Z')[source]

Multi-sample/replicate implement of scReadSim for constructing count matrices for scRNA-seq BAM file.

Parameters:

  • cells_barcode_file (str) – List of cell barcode files corresponding to the input BAM files.

  • INPUT_bamfile (str) – List of input BAM files (use absolute paths to the BAM files).

  • outdirectory (str) – Specify the working directory of scReadSim for generating intermediate and final output files.

  • n_cores (int (default: 1)) – Specify the number of cores for parallel computing when generating count matrix.

  • UMI_modeling (bool (default: True)) – Specify whether scReadSim should model UMI count of the input BAM file.

  • UMI_tag (str (default: ‘UB:Z’)) – If UMI_modeling is set to True, specify the UMI tag of input BAM file, default value ‘UB:Z’ is the UMI tag for 10x scRNA-seq.