scReadSim.Utility.scRNA_CreateFeatureSets

scReadSim.Utility.scRNA_CreateFeatureSets(INPUT_bamfile, samtools_directory, bedtools_directory, outdirectory, genome_annotation, genome_size_file)[source]

Create the foreground and background feature set for the input scRNA-seq bam file.

Parameters:

  • INPUT_bamfile (str) – Input BAM file.

  • samtools_directory (str) – Path to software samtools.

  • bedtools_directory (str) – Path to software bedtools.

  • outdirectory (str) – Specify the output directory of the features files.

  • genome_annotation (str) – Genome annotation file for the reference genome that the input BAM aligned on or the synthetic BAM should align on.

  • genome_size_file (str) – Genome sizes file. The file should be a tab delimited text file with two columns: first column for the chromosome name, second column indicates the size.