rakarnik / moabs

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data

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-v1.3.0.src.x86_64_Linux.data.tar.gz

If you download the source from github: The data files in folder bin/ have been deleted in github repository due to size limit. Please make sure you download them and put them in bin/ folder.

##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 setting replicate variance containing biological variance

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 [email protected].

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