bismark_methylation_extractor

This function is used for extracting methylation information from bismark output.

Note

This function is calling bismark.

bismark official docs

Krueger, Felix, and Simon R. Andrews. “Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.” bioinformatics 27.11 (2011): 1571-1572.

Parameters

bismark_methylation_extractor(bamInput=None, outputdir=None, threads=1,
            other_params={
                "--no_overlap": True,
                "--report": True,
                "--no_header": True,
                "--gzip": True,
                "--bedGraph": True,
                "--zero_based": True,
            }, paired=True, stepNum=None, upstream=None, verbose=True)
  • bamInput: list, input bam files.

  • outputdir: str, output result folder, None means the same folder as input files.

  • threads: int, how many thread to use.

  • paired: True for paired data, False for single end data.

  • other_params: dict, other parameters passing to FASTQC.

    “-parameter”: True means “-parameter” in command line. “-parameter”: 1 means “-parameter 1” in command line.

  • stepNum: int or str, step flag for folder name.

  • upstream: upstream output results, used for pipeline.

  • verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

Example usage:

# bam file must from bismark or bismark_deduplicate output and not be sorted!
bams = ["test1.bam", "test2.bam"]

bismark_methylation_extractor(bamInput=bams, paired=True)