bismark

This function is used for mapping WGBS data.

Note

This function is calling bismark, we will set multicore in bismark, do not use prefix paramter in 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(seqInput1=None, seqInput2=None,
        ref=None, outputdir=None,
        threads=1, paired=True,
        other_params={"-q": True, "--phred33-quals": True, "--bowtie2": True, "--un": True,},
        stepNum=None, upstream=None, verbose=True)

  • seqInput1: list, input _1 fastq files.

  • seqInput2: list, input _2 fastq files, None for single end.

  • ref: bismark reference path.

  • 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 Bismark.

    “-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. This parameter can be True, which means a new pipeline start.

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

Example usage:

fq1 = ["test1_1.fq", "test2_1.fq"]
fq2 = ["test1_2.fq", "test2_2.fq"]

bismark(seqInput1=fq1, seqInput2=fq2,
        ref="path_to_bismark_genome",
        threads=30, paired=True)