scReadSim.scRNA_GenerateBAM.scRNA_GenerateBAMCoord

scReadSim.scRNA_GenerateBAM.scRNA_GenerateBAMCoord(bed_file, UMI_count_mat_file, synthetic_cell_label_file, read_bedfile_prename, INPUT_bamfile, outdirectory, OUTPUT_cells_barcode_file, jitter_size=5, read_len=90, UMI_tag='UB:Z')[source]

Generate Synthetic reads in BED format.

Parameters:

  • bed_file (str) – Features’ bed file to generate the synthetic reads (Generated by function Utility.scRNA_CreateFeatureSets).

  • UMI_count_mat_file (str) – The path to synthetic UMI count matrix.

  • synthetic_cell_label_file (str) – Synthetic cell label file generated by scRNA_GenerateSyntheticCount.

  • read_bedfile_prename (str) – Specify the base name of output bed file.

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

  • outdirectory (str) – Specify the output directory for synthetic reads bed file.

  • OUTPUT_cells_barcode_file (str) – Specify the file name storing the synthetic cell barcodes.

  • jitter_size (int (default: ‘5’)) – Specify the range of random shift to avoid replicate synthetic reads. Default value is 5 bp.

  • read_len (int (default: ‘90’)) – Specify the length of synthetic reads. Default value is 90 bp.

  • 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.