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Archived Comments for: ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

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  1. Underlying mapping algorithm Batman still unpublished.

    Alejandro Fernandez, Karolinska Institutet

    4 March 2015

    "After linker trimming, the tags are mapped to the corre-sponding reference genome using the Batman package (CTennakoon et al., manuscript submitted) with at most one mismatch."  

    I was unable to find references or any documentation regarding Batman, has this been documented? Does the tool work with BWA or Bowtie? 


    Competing interests

    None declared
  2. The updated ChIA-PET Tool

    Guoliang Li, None declared

    22 January 2016

    and the mapping tool

    Competing interests

    The updated ChIA-PET Tool is available at GitHub ( In the original package, a Burrows-Wheeler-transform-based method BatMan (later updated and renamed to BatMis in its published version) was used to generate customized output format. In the current ChIA-PET Tool package, any state-of-the-art mapping methods can be used for mapping, as long as the output is in SAM/BAM format. In our pipeline, BWA with the default parameters is used for mapping the short reads in paired-end mode, which can be replaced by other mapping tools.

    Tennakoon, C., Purbojati, R. W. & Sung, W. K. BatMis: a fast algorithm for k- mismatch mapping. Bioinformatics 28, 2122-2128, doi:10.1093/bioinformatics/bts339 (2012)