How to use

How to use#

Installation#

The full name of pattools is pattools-methy. This naming was chosen because the name pattools was already taken on PyPI. There are several ways to install pattools

Install from PyPI#

pip install pattools-methy

Install from github#

pip install git+https://github.com/hcyvan/pattools.git

Install from source#

Download the source code, and then

cd /path/to/source/code
pip install -r requirements.txt
python ./setup.py install

Usage#

fishy

Once the installation is complete, you can begin analyzing BS-seq data. The general workflow involves the following steps:

  1. Prepare the Reference Genome: Build the appropriate reference genome based on the species being analyzed.

eg:

pattools reference -f /PathTo/hg38.fa.gz -o /OutputPathTo/hg38 -c chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM

  1. Convert Data to PAT Format: Convert the BS-seq data to the PAT format for compatibility with further processing.

  2. Conduct Downstream Analysis: Perform additional analysis steps based on your specific research needs and objectives.

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