Meta-epigenomic analysis

Table of contents

• Overview
• Prerequisites
• Getting MTase and motif information from REBASE
• Simple example
• Documentation: Motif calculation
• Documentation: Overlapped_SNMV

Overview

This toolkit helps detect DNA methylation patterns across metagenomic samples.

Prerequisites

• The metagenome-assembled genomes (MAGs) must be prepared prior to analysis as this is based on genome-centric metagenomics.

• This analysis requires the results of the base modification (ipdSummary) results from PacBio sequencing (https://libraries.io/github/ben-lerch/BaseMod-3.0).

• Commands what I used for the ipdSummary is available here.

• The absolute paths of bedtools and samtools must be written in the program.txt file as follows:

bedtools:[/usr/bin/bedtools] #(tested by bedtools v2.25.0)
samtools:[/usr/bin/samtools] #(tested by htslib 1.8)

• Required python 3.6 >= and libraries

Using the command of pip3 install [somthing]

re, itertools, optparse, shutil, pathlib, gzip, pickle, tqdm, biopython

Then, please copy this git

git clone https://github.com/hoonjeseong/Meta-epigenomics.git

• MTases and their motif information

If you want to get the motif of DNA methylation patterns reported in REBASE, then I suggest you access the analysis in Getting MTase and motif information from REBASE. It provides motif information recognized by methyltransferases (MTases) in the REBASE database, for example in the form of G_A_NTC/G_A_NTC (forward/reverse strand).

Simple example

• Motif calculation: The purpose of this script is to obtain methylated frequency of each motif on MAGs across metagenomic samples.

Documentation: Motif calculation

Usage: python Motif_calculation.py -b [bam; folder of bamfiles; Extension: bam] -i [folder of ipdSummary files; Extension: gff] -g [folder of MAGs; Extension: fa or fna] -o [output]

• SNMV comparison in overlapped region: The purpose of this script is to calculate the fraction of specific methylated motif by each nucleotide position on MAGs across metagenomic samples.

Documentation: Overlapped_SNMV

Usage: python Overlapped_SNMV.py -i [folder of ipdSummary files; Extension: csv and gff] -g [folder of MAGs; Extension: fa or fna] -m motif [fwd/rev] -o [output]