scReadSim.scATAC_GenerateBAM.scATAC_BED2FASTQ

scReadSim.scATAC_GenerateBAM.scATAC_BED2FASTQ(bedtools_directory, seqtk_directory, referenceGenome_file, outdirectory, BED_filename_combined, synthetic_fastq_prename)[source]

Convert Synthetic reads from BED to FASTQ.

Parameters:

  • bedtools_directory (str) – Directory of software bedtools.

  • seqtk_directory (str) – Directory of software seqtk.

  • referenceGenome_file (str) – Directory of the reference genome FASTA file that the synthteic reads should align.

  • outdirectory (str) – Output directory of the synthteic bed file and its corresponding cell barcodes file.

  • BED_filename_combined (str) – Specify the base name of output bed file of function ‘scATAC_CombineBED’.

  • synthetic_fastq_prename (str) – Specify the base name of the output FASTQ files.