scReadSim.Utility.scRNA_bam2countmat_paral

scReadSim.Utility.scRNA_bam2countmat_paral(cells_barcode_file, bed_file, INPUT_bamfile, outdirectory, count_mat_filename, UMI_modeling=True, UMI_tag='UB:Z', n_cores=1)[source]

Construct read (or UMI) count matrix for scRNA-seq BAM file.

Parameters:

  • cells_barcode_file (str) – Cell barcode file corresponding to the input BAM file.

  • bed_file (str) – Features bed file to generate the count matrix.

  • INPUT_bamfile (str) – Input BAM file for anlaysis.

  • outdirectory (str) – Specify the output directory of the count matrix file.

  • count_mat_filename (str) – Specify the base name of output read (or UMI) 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.

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