scReadSim.scRNA_GenerateBAM.scRNA_BED2FASTQ

scReadSim.scRNA_GenerateBAM.scRNA_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) – Path to software bedtools.

  • seqtk_directory (str) – Path to software seqtk.

  • referenceGenome_file (str) – 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) – Base name of the combined bed file output by function scRNA_CombineBED.

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