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moabs
MOABS: MOdel based Analysis of Bisulfite Sequencing data
A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing.
Abstract
MOABS seamlessly integrates alignment, methylation calling, identification of hypomethylation for one sample and differential methylation for multiple samples, and other downstream analysis.
Comprehensive Document
The PDF version is available at
http://dldcc-web.brc.bcm.edu/lilab/deqiangs/moabs/moabs-v1.2.2.pdf
The online HTML version created from 'latex2html' command is available at
http://dldcc-web.brc.bcm.edu/lilab/deqiangs/moabs/moabs.html
Download
The source code, prebuilt binary on x86_64 Linux system, and test data
https://s3.amazonaws.com/deqiangsun/software/moabs/moabs-v1.3.2.src.x86_64_Linux.data.tar.gz https://s3.amazonaws.com/deqiangsun/software/moabs/moabs-v1.3.2.src.x86_64_Linux.data.no_database.tar.gz
Installation of prebuilt binaries
Download moabs-v1.3.0.src.x86_64_Linux.data.tar.gz to /your/path/, Add the bin/ to your $PATH variable by command export PATH=/your/path/moabs-v1.3.0.src.x86_64_Linux.data/bin/:$PATH, Then use the prebuilt executables in bin/ ! Note the moabs path need be in front of $PATH because there is a system program named mcomp too.
Please do not move or copy mcomp to a different location because it need to read the database files in the same directory.
Installation from source codes
You need install the Perl module Config::Simple for the pipeline. This module is not required if you use individual modules.
cd moabs-v1.3.0.src.x86_64_Linux.data
make
make install
The make command will compile source files and generate system dependent dynamic binary executables. The make install command will overwrite the static binaries in moabs-v1.3.0.src.x86_64_Linux.data/bin/ with the dynamic ones.
You need also export PATH=/your/path/moabs-v1.3.0.src.x86_64_Linux.data/bin/:$PATH to use the command without involving full path.
If you encounter make errors, please contact us.
Fast Manual
One may go to the test/ and type moabs --cf mytestrun.cfg
to get started if you have installed the Perl Config::Simple module. In addition, you may also directly use the binary for each individual function in the moabs-v1.2.3/bin/.
In short, one may simply finish the whole processing of bisulfite data for two conditions by typing
moabs --cf my_research_config_file
or
moabs -i wt_r1.fq -i wt_r2.fq -i ko_r1.fq -i ko_r2.fq
Done!
An example use of individual module mcomp
cd test/
../bin/mcomp -r wt_r1.bam.G.bed,wt_r2.bam.G.bed -r ko_r1.bam.G.bed,ko_r2.bam.G.bed -m wildtype -m knockout -c comp.wiVar.txt --withVariance 1 -p 4
Cite Our Paper
Deqiang Sun, Yuanxin Xi, Benjamin Rodriguez, Hyun Jung Park, Pan Tong, Mira Meong, Margaret A Goodell and Wei Li. MOABS: model based analysis of bisulfite sequencing data. Genome Biology, 15 (2014)
Link:http://genomebiology.com/2014/15/2/R38/abstract
Contact
The package is developed by Deqiang Sun. Please post any questions, suggestions or problems to the MOABS Discussion google group or send email to Deqiang Sun at moabs_msuite@googlegroups.com.
You are welcome to subscribe to the moabs MOABS Discussion google group for updates.
Related projects
mSuite: DNA Methylation analysis in one Suite , which packages ExactNumCI, MOABS, MEPS and other tools.
MEPS: MEthylation Pipeline and Service on cloud
Project Information
The project was created on Jun 12, 2013.
- License: GNU GPL v3
- 5 stars
- git-based source control
Labels:
Bioinformatics
Sequence
Methylation
Hydroxymethylation
Bisulfite
RRBS
WGBS
DMR
DMC
HMR
Hypomethylation
Differential