scReadSim.scATAC_GenerateBAM.scATAC_GenerateBAMCoord_OutputPeak

scReadSim.scATAC_GenerateBAM.scATAC_GenerateBAMCoord_OutputPeak(target_peak_assignment_file, count_mat_file, synthetic_cell_label_file, read_bedfile_prename, INPUT_bamfile, outdirectory, OUTPUT_cells_barcode_file, jitter_size=5, read_len=50, random_noise_mode=False)[source]

Generate Synthetic reads in BED format.

Parameters:

  • target_peak_assignment_file (str) – Mapping file between input peaks and output peaks, output by ‘FeatureMapping’.

  • count_mat_file (str) – The path to the synthetic count matrix generated by GenerateSyntheticCount.scATAC_GenerateSyntheticCount.

  • synthetic_cell_label_file (str) – Synthetic cell label file generated by scATAC_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: ‘50’)) – Specify the length of synthetic reads. Default value is 50 bp.

  • random_noise_mode ('bool' (default: 'False')) – Specify whether to use a uniform distribution of reads.