scReadSim.scRNA_GenerateBAM.AlignSyntheticBam_Single

scReadSim.scRNA_GenerateBAM.AlignSyntheticBam_Single(bowtie2_directory, samtools_directory, outdirectory, referenceGenome_name, referenceGenome_dir, synthetic_fastq_prename, output_BAM_pre)[source]

Convert Synthetic reads from FASTQ to BAM.

Parameters:

  • bowtie2_directory (str) – Path to software bowtie2.

  • samtools_directory (str) – Path to software samtools.

  • outdirectory (str) – Specify the output directory of the synthteic BAM file.

  • referenceGenome_name (str) – Base name of the eference genome FASTA file. For example, you should input “chr1” for file “chr1.fa”.

  • referenceGenome_dir (str) – Path to the reference genome FASTA file.

  • synthetic_fastq_prename (str) – Base name of the synthetic FASTQ file output by function scRNA_BED2FASTQ.

  • output_BAM_pre (str) – Specify the base name of the output BAM file.