scReadSim.scRNA_GenerateBAM.scRNA_GenerateSyntheticRead_MultiSample

scReadSim.scRNA_GenerateBAM.scRNA_GenerateSyntheticRead_MultiSample(INPUT_bamfile, outdirectory, bedtools_directory, seqtk_directory, fgbio_jarfile, referenceGenome_file, read_len=90)[source]

Multi-sample/replicate implement of scReadSim for simulating scRNA-seq synthetic reads.

Parameters:

  • INPUT_bamfile (str) – List of input BAM files (use absolute paths to the BAM files).

  • outdirectory (str) – Specify the working directory of scReadSim for generating intermediate and final output files.

  • bedtools_directory (str) – Directory of software bedtools.

  • seqtk_directory (str) – Directory of software seqtk.

  • fgbio_jarfile (str) – Path to software fgbio jar script.

  • referenceGenome_file ('str') – Reference genome FASTA file that the synthteic reads should align.

  • read_len (int (default: ‘90’)) – Specify the length of synthetic reads. Default value is 90 bp.