A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing.
MOABS has been deployed in https://anaconda.org/bioconda/moabs. To install MOABS from Bioconda, the following channels should be added. Namely,
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install moabsMOABS has been depolyed in https://usegalaxy.eu/root?tool_id=moabs for public usage.
MOABS seamlessly integrates alignment, methylation calling, identification of hypomethylation for one sample and differential methylation for multiple samples, and other downstream analysis.
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
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.
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 $PATH because there is a system program named mcomp too.
Please do not move or copy mcomp to a different location because it need to read the database files in the same directory.
You need install the Perl module Config::Simple for the pipeline. This module is not required if you use individual modules.
cd moabs-v1.3.0.src.x86_64_Linux.data
make
make install The make command will compile source files and generate system dependent dynamic binary executables. The make install command will overwrite the static binaries in moabs-v1.3.0.src.x86_64_Linux.data/bin/ with the dynamic ones.
You need also export PATH=/your/path/moabs-v1.3.0.src.x86_64_Linux.data/bin/:$PATH to use the command without involving full path.
If you encounter make errors, please contact us.
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_fileor
moabs -i wt_r1.fq -i wt_r2.fq -i ko_r1.fq -i ko_r2.fqDone!
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 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
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.
mSuite: DNA Methylation analysis in one Suite, which packages ExactNumCI, MOABS, MEPS and other tools.
MEPS: MEthylation Pipeline and Service on cloud