ASM-Detector

v1.0.0-alpha

1.Introduction

ASM-Detector implements a novel computational method to better detect ASMs from whole-genome bisulfite sequencing (WGBS) data. It takes SAM format mapped reads along with FASTA format reference genome as input. In the first step, a serie of parameters are used to select the condidate ASM regions with high quality. Then our graph-based clustering method is applied to detect ASM regions. The output of ASM-Detector includes summary of all detected ASM regions and reads partition results of each ASM region, which can be used in downstream analysis. ASM-Detector also provides several useful tools to perform further analysis of ASM regions, such as visulizing ASM regions in figure.

2.Prerequisite

• Java 1.8 or higher

2.1 install

Unzip ASM-detector.zip file. Executable files are under bin folder.

To add ASM-detector to $PATH, check here

3 Demo

Download demo data

Demo folder structure:

.
├── chr8.fa
└── TRAPPC9_ads_adipose.sam

All following command are executed in demo folder. Assuming ASM-Detector required softwares are setup properly(added to $PATH). You can also execute commands through relative path, e.g. ../bin/cpmr, which assume bin folder is in the same level of demo folder.

3.1 cpmr: generate candidate ASM regions

>cpmr -m TRAPPC9_ads_adipose.sam -r chr8.fa -mcc 4 -mic 5 -mir 10 -p 0.3 --format sam -o TRAPPC9 -pe
Load refChr chr8-0-146364021 with 1309135 RefCpGs. Complete in 2.412000 s
Load 4601 Mapped Reads. Complete in 0.249000 s

After execution, demo folder looks like:

.
├── chr8.fa
├── TRAPPC9
│   ├── chr8-141108112-141109094.mappedreads
│   ├── chr8-141109226-141110677.mappedreads
│   ├── chr8-141110686-141111080.mappedreads
│   ├── CPMR.bed
│   └── CPMR.report
└── TRAPPC9_ads_adipose.sam

3.2 asmd: detect ASM regions

>asmd -i TRAPPC9 -mic 5 -p 100 -t 8 -o TRAPPC9_result

After execution, demo folder looks like:

.
├── chr8.fa
├── TRAPPC9
│   ├── chr8-141108112-141109094.mappedreads
│   ├── chr8-141109226-141110677.mappedreads
│   ├── chr8-141110686-141111080.mappedreads
│   ├── CPMR.bed
│   └── CPMR.report
├── TRAPPC9_ads_adipose.sam
└── TRAPPC9_result
    ├── chr8-141108112-141109094.mappedreads.detected
    ├── chr8-141108112-141109094.mappedreads.groups.aligned
    ├── chr8-141109226-141110677.mappedreads.detected
    ├── chr8-141109226-141110677.mappedreads.groups.aligned
    ├── chr8-141110686-141111080.mappedreads.detected
    ├── chr8-141110686-141111080.mappedreads.groups.aligned
    └── detection.summary

3.3 mfig: generate methylation figure base on aligend reads file.

>mfig  -i TRAPPC9_result/chr8-141109226-141110677.mappedreads.groups.aligned -p 141109990 -a T-G -s 22

Output is in the same folder of input file with file name extension ".compact.eps". Example: chr8-141109226-141110677.mappedreads.groups.aligned.compact.eps

4.Interface

4.1 cpmr:

usage: cpmr [options]
    --format <arg>   specify format of input: mappedread, sam
 -m <arg>            MappedRead File (Required)
 -mcc <arg>          Minimum adjacent CpG coverage (Required)
 -mic <arg>          Minimum interval CpG number (Required)
 -mir <arg>          Minimum interval read number (Required)
 -o <arg>            Output Path (Required)
 -p <arg>            Partial methylation threshold (Required)
 -pe                 Pair end mode (Optional)
 -r <arg>            Reference File (Required)

4.2 asmd:

usage: asmd [options]
 -i <arg>     Input intervals folder or interval file name (Required)
 -mic <arg>   Minimum interval CpG number (Required)
 -o <arg>     output folder. Will be create if not exist (Required)
 -p <arg>     Time of random permutation (Required)
 -t <arg>     Thread number to call the program (Required)

4.3 mfig:

usage: mfig [options]
 -a <arg>   allele pair. E.g. A-G
 -i <arg>   input grouped read file
 -p <arg>   SNP position
 -s <arg>   font size

5.Output

5.1 cpmr output

CPMR.bed

Bed file contains every CPMR regions and their read count/cpg count.

Individual CPMR region read file

Contains reference sequnece and reads with columns(ref,strand,start,end,sequence,ID)

5.2 asmd output

detection.summary

Bed file contains each ASM region detected.

.detected file

Contains p-value, average methylation information and covered read count(in bracket) of each CpG site in every groups.

.groups.aligned file

Similar to CPMR region file. However reads in this file are aligned by coordinates and separated into groups for visulization purpose.

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Citation

Hu, K., & Li, J. Allele-specific DNA methylation is ubiquitous in human genome and is highly associated with transcriptional regulation (Under Review)

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License

Copyright 2017 © Computational Biology lab @ Case Western Reserve University. See the LICENSE file for license rights and limitations (GPL v3).