l Installation

Users can get FastDMA version 1.2.0 from http://bioinfo.au.tsinghua.edu.cn/software/fastdma. To install it, users can download the fastdma-1.2.0-full.tar.gz file and need a GNU/Linux system. For non-experts in GNU/Linux system, please follow the installation guideline carefully.

1) Unzip fastdma-1.2.0-full.tar.gz using the following command:

tar zxf fastdma-1.2.0-full.tar.gz

2) Enter the fastdma directory.

cd fastdma-1.2.0

3) Run the installation script to install FastDMA at directory <installation_absolute_path> (please use absolute path). Because the boost and gsl library need to be installed for the first time, this step can be time consuming.

chmod u+x fastdma-install

./fastdma-install <installation_absolute_path>

4) Export the shared libraries directories

source ~/.bashrc

5) Check the directory <installation_absolute_path>, make sure that there is a bin directory under <installation_absolute_path> and two files “fastdma” and “split” under the bin directory.

./bin/fastdma

to see whether there is help information. If the help information appears, it implies that you have installed FastDMA successfully.

l Testing

1) Please move the data folder unzipped from fastdma-1.2.0-full.tar.gz under <installation_absolute_path>. All the testing data are under the data folder.

mv <unzip path>/fastdma-1.2.0/data <installation_absoulte_path>

2) To create the formatted input files required by FastDMA, please enter the <installation_absolute_path> and run

./bin/split –d ./data ./data/test_data.txt

3) Create a folder saving the resultant files.

mkdir result

4) Run FastDMA

./bin/fastdma -p 0.01 -q 0.01 --unify -n 2 -c data/test_configure.txt --covariable 2 --probe data/test_probe_ann.txt --op result/probe.txt --probe-prefix result/probe --cgi data/test_cpgIsland.txt --oc result/cgi.txt --cgi-prefix result/cgi --od result/dmr.txt --dmr-prefix result/dmr

5) If everything is OK, you will see many files under the result folder:

probe.txt => the differentially methylated probes

cgi.txt => the differentially methylated CpG islands (or any pre-defined regions)

dmr.txt => the differentially methylated regions using sliding windows

For further explanations of all these files and steps. Please see the user manual or contact with wdm2008@gmail.com, wellgoo@gmail.com.