scReadSim.scATAC_GenerateBAM.scATAC_ErrorBase

scReadSim.scATAC_GenerateBAM.scATAC_ErrorBase(fgbio_jarfile, INPUT_bamfile, referenceGenome_file, outdirectory, synthetic_fastq_prename)[source]

Introduce random substitution errors into synthetic reads according to real data error rates.

Parameters:

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

  • INPUT_bamfile (str) – Input BAM file for anlaysis.

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

  • outdirectory (str) – Specify the output directory of the synthteic FASTQ file with random errors.

  • synthetic_fastq_prename (str) – Base name of the synthetic FASTQ files output by function scATAC_BED2FASTQ.