bismark_deduplicate

This function is used for removing duplicates 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_deduplicate(bamInput=None, outputdir=None,
                    threads=1, paired=True,
                    other_params={}, 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 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:

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

bismark_deduplicate(bamInput=bams, paired=True)