Introduction

This program summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor. Information of the DNA methylation positions for each amplicon, DNA methylation patterns observed within each amplicon and their abundance counts are summarised into a tab delimited text file amenable for further downstream statistical analysis. Methpat also outputs a HTML file containing visualisations of the methylation pattern data.

Homepage

The homepage for methpat contains additional information about the program.

License

Methpat is released as open source software under the terms of the 3 clause BSD License. See the file LICENCE.txt in the source code repository of methpat.

Installation

Methpat currently requires version 2.7 of Python.

The best way to install Methpat is to use the following command:

pip install git+https://github.com/bjpop/methpat.git

This will automatically download and install the dependencies of methpat.

Usage

usage: methpat [-h] [--version] [--count_thresh THRESH] --amplicons
               AMPLICONS_FILE [--logfile FILENAME] [--html FILENAME]
               [--webassets {package,local,online}] [--title TITLE]
               [--filterpartial] [--min_cpg_percent PERCENT]
               BISMARK_FILE

Summarise methylation patterns in bismark output, and generate visualisation.

positional arguments:
  BISMARK_FILE          input bismark file

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --count_thresh THRESH
                        only display methylation patterns with at least THRESH
                        number of matching reads, defaults to "0"
  --amplicons AMPLICONS_FILE
                        file containing amplicon information in TSV format
  --logfile FILENAME    log progress in FILENAME, defaults to "methpat.log"
  --html FILENAME       save visualisation in html FILENAME defaults to
                        "methpat.html"
  --webassets {package,local,online}
                        location of assets used by output visualisation web
                        page, defaults to "package"
  --title TITLE         title of the output visualisation page, defaults to
                        "Methylation Patterns"
  --filterpartial       Ignore reads which contain (at least one) unknown
                        methylation status
  --min_cpg_percent PERCENT
                        only consider CPG sites which occur at least PERCENT
                        of reads for an amplicon