Discovering local read-level DNA methylation patterns and DNA methylation heterogeneity in intermediately methylated regions

Overview

MeConcord

  • MeConcord is a method used to investigate local read-level DNA methylation patterns for intermediately methylated regions with bisulfite sequencing data.
  • Intermediately methylated regions occupy a significant fraction of the whole genome and are markedly associated with epigenetic regulations or cell-type deconvolution of bulk data. However, these regions show distinct methylation patterns corresponding to different biological mechanisms. Although there have been some metrics developed for investigating these regions, the poor perfor-mance in antagonizing noises limits the utility for distinguishing distinct methylation patterns.
  • We proposed a method, MeConcord, with two metrics measuring local methylation concordance across reads and CpGs, respectively, with Hamming distance. MeConcord showed the most robust performance in distinguishing distinct methylation patterns (identical, uniform, and disor-dered) compared with other metrics.

Installation

  • MeConcord is implemented by Python and compatible with both Python 2 and Python 3.
  • Modules of python are required:pysam(if the input is .bam files), pandas,numpy, scipy,multiprocessing.
  • The scripts could be downloaded and used directly with command python *.py -i ....

Usage

Input

MeConcord currently only accept the output(.bam or converted to .sam) of Bismark (https://github.com/FelixKrueger/Bismark/blob/master/README.md)

Run

1.Obtaining CpG positions across genome

Usage: python pre_cpg_pos.py -i hg38.fa -o ./cpg_pos/

  • i, The path to reference sequences (.fa);
  • o, The path that you want to deposit the positions of CpG sites, each chromosome has a seperate file;
  • h, Help information

2.Converting mapped Bam, Sam, Sam.gz files from Bismark to methylation recordings read-by-read

Usage: python s1_bamToMeRecord.py -i test.bam -o test -c 0

  • i, The path to input files (.bam or .sam or .sam.gz);
  • o, Output prefix;
  • c, Clipping read ends with such base number (defalut 0); can be used when sequencing quality of read ends is not good. such as -c 5 to remove 5 bases from the both ends of the reads.
  • h, Help information

3.Spliting the big MeRecord files into small files of each chromosome to redude memory requirements in the next step

Usage: python s2_RecordSplit.py -i ./test_ReadsMethyAndMuts.txt -o ./test -g chr1,chr2,chr3,chr4,chr5

  • i, The path to s1 output. ( end with _ReadsMethyAndMuts.txt);
  • o, Output prefix;
  • g, Chromosomes used; (default chromsome 1-22); chromosomes shoud be seperated by comma;
  • h, Help information

4. Calculating concordance metrics (NRC, NCC and P-values)

Usage: python s3_RecordToMeConcord.py -p 4 -i ./test -o ./test -r ./region.bed -c ./cpgpos/ -b 150 -m 600 -z 0 -g chr1,chr2,chr3

  • i, The path to s2_RecordSplit.py output, with prefixed file name;
  • p, Threads used for parallel computation; default is 4;
  • o, Output prefix;
  • r, The files with genomic regions for computation, chrom, start, end seperated by tab;
  • c, Cpg position folder, output of pre_cpg_pos.py;
  • b, Bin size (default 150bp);
  • z, Whether is the genomic file based on 0; 0 (default) or 1; output is same to input bins; if -r is a bed file, -z should be 1;
  • g, Chromosomes used; (default chromsome 1-22); chromosomes shoud be seperated by comma;
  • m, Maximum of fragement length in sequencing library(default 600bp for paired-end reads). if there are single-end reads,m should be set as the length of reads, if not sure, default will work for most cases;

5. Methylation recordings to methylation matrix (optional)

Usage: python s4_RecordToMeMatrix.py -i ./test -o ./test -r ./p1.bed -c ./cpgpos/ -m 600 -z 0 -g chr1,chr2

  • i, The path to s2_RecordSplit.py output, with prefixed file name;
  • o, Output prefix;
  • r, The files with genomic regions for computation, chrom, start, end seperated by tab;
  • c, Cpg position folder, output of pre_cpg_pos.py;
  • z, Whether is the genomic file based on 0; 0 (default) or 1; output is same to input bins; if -r is a bed file, -z should be 1;
  • g, Chromosomes used; (default chromsome 1-22); chromosomes shoud be seperated by comma;
  • m, Maximum of reads length (default 600bp for paired-end reads). if there are single-end reads,m should be set length of reads, if not sure, default will work for most cases;

6. Visualization of methylation matrix (optional)

Usage: visualization_Matlab.m

  • Open this script and edit

    • path_to_matrix as the path you deposit the MeMatrix;
    • path_to_cpgPos as the path you deposit CpG positions of the genome, which is the result of pre_cpg_pos.py;
    • name as the name of MeMatrix, for example 'test_chr1_1287967_1288117';
  • Output: two lollipop plots, one without considering distance between CpGs, one considering distance between CpGs.

    • unmethylated CpGs are labeled as light blue
    • CpGs without signal are labeled as grey
    • methylated CpGs are labeled as dark red

Test for an example

  • STEP 1 python s1_bamToMeRecord.py -i ./test/GM12878_chr1_1286017_1294783.bam -o ./test/test -c 2 or python s1_bamToMeRecord.py -i ./test/GM12878_chr1_1286017_1294783.sam -o ./test/test -c 2 if there is no pysam module on Windows

    • The error that Could not retrieve index file for './test/GM12878_chr1_1286017_1294783.bam' doesn't affect the results.
    • Please check if there is an output in test folder, test_ReadsMethyAndMuts.txt. If yes, it works.
  • STEP 2 python s2_RecordSplit.py -i ./test/test_ReadsMethyAndMuts.txt -o ./test/test -g chr1

    • Please check if there is an output in test folder, test_ReadsMethyAndMuts_chr1.txt. If yes, it works.
  • STEP 3 python s3_RecordToMeConcord.py -p 1 -i ./test/test -o ./test/test -r ./test/tmp1.bed -c ./test/ -b 150 -m 600 -z 1 -g chr1

    • Please check if there is an output in test folder, test_MeConcord.txt. If yes, it works.
  • STEP 4 python s4_RecordToMeMatrix.py -i ./test/test -o ./test/test -r ./test/tmp2.bed -c ./test/ -m 600 -z 1 -g chr1

    • Please check if there is two output files in test folder, test_chr1_1287967_1288117_me.txt; test_chr1_1287967_1288117_unme.txt. If yes, it works.
Owner
omics tools,especially for DNA methylation
The Official Jaseci Code Repository

Jaseci Release Notes Version 1.2.2 Updates Added new built-ins for nodes and edges (context, info, and details) Fixed dot output Added reset command t

136 Dec 20, 2022
PIP Manager written in python Tkinter

PIP Manager About PIP Manager is designed to make Python Package handling easier by just a click of a button!! Available Features Installing packages

Will Payne 9 Dec 09, 2022
A Python software implementation of the Intel 4004 processor

Pyntel4004 A Python software implementation of the Intel 4004 processor. General Information Two pass assembler using the original mnemonics, directiv

alshapton 5 Oct 01, 2022
Python with braces. Because Python is awesome, but whitespace is awful.

Bython Python with braces. Because Python is awesome, but whitespace is awful. Bython is a Python preprosessor which translates curly brackets into in

1 Nov 04, 2021
Vaksina - Vaksina COVID QR Validation Checker With Python

Vaksina COVID QR Validation Checker Vaksina is a general purpose library intende

Michael Casadevall 33 Aug 20, 2022
This collection is to provide an easier way to interact with Juniper

Ansible Collection - cremsburg.apstra Overview The goal of this collection is to provide an easier way to interact with Juniper's Apstra solution. Whi

Calvin Remsburg 1 Jan 18, 2022
msImpersonate - User account impersonation written in pure Python3

msImpersonate v1.0 msImpersonate is a Python-native user impersonation tool that is capable of impersonating local or network user accounts with valid

Joe Helle 90 Dec 16, 2022
Functional interface for concurrent futures, including asynchronous I/O.

Futured provides a consistent interface for concurrent functional programming in Python. It wraps any callable to return a concurrent.futures.Future,

A. Coady 11 Nov 27, 2022
nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

150 Jan 07, 2023
VHDL to Discrete Logic on PCB Flow

PCBFlow Highly experimental set of scripts to transform a digital circuit described in a hardware description language (VHDL or Verilog) into a discre

Tim 77 Nov 04, 2022
SQL centered, docker process running game

REQUIREMENTS Linux Docker Python/bash set up image "docker build -t game ." create db container "run my_whatever/game_docker/pdb create" # creating po

1 Jan 11, 2022
A complex language with high level programming and moderate syntax.

zsq a complex language with high level programming and moderate syntax.

an aspirin 6 Jun 25, 2022
In this repo i inherit the pos module and added QR code to pos receipt

odoo-pos-inherit In this repo i inherit the pos module and added QR code to pos receipt 1- Create new Odoo Module using command line $ python odoo-bin

5 Apr 09, 2022
A lightweight Python module to interact with the Mitre Att&ck Enterprise dataset.

enterpriseattack - Mitre's Enterprise Att&ck A lightweight Python module to interact with the Mitre Att&ck Enterprise dataset. Built to be used in pro

xakepnz 7 Jan 01, 2023
Build Xmas cards with user inputs

Automatically build Xmas cards with user inputs

Anand 9 Jan 25, 2022
Web app to find your chance of winning at Texas Hold 'Em

poker_mc Web app to find your chance of winning at Texas Hold 'Em A working version of this project is deployed at poker-mc.ue.r.appspot.com. It's run

Aadith Vittala 7 Sep 15, 2021
A simple bot that will help you in your learning and make it more fun.

hyperskill-SimpleChattyBot-python A simple bot that will help you in your learning and make it more fun. Syntax bot.py Stages Stage #1: Zuhura Bot we

1 Nov 09, 2021
J MBF - Assalamualaikum Mamang...

★ VISITOR ★ ★ INFORMATION ★ Script Ini DiBuat Oleh YayanXD Script Ini Akan DiPerjual Belikan Tanggal 9 Januari 2022 Jika Mau Beli Script Silahkan Hub

Risky [ Zero Tow ] 5 Apr 08, 2022
一个Graia-Saya的插件仓库

一个Graia-Saya的插件仓库 这是一个存储基于 Graia-Saya 的插件的仓库 如果您有这类项目

ZAPHAKIEL 111 Oct 24, 2022
Graphsignal Logger

Graphsignal Logger Overview Graphsignal is an observability platform for monitoring and troubleshooting production machine learning applications. It h

Graphsignal 143 Dec 05, 2022