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.
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
4) Export the shared libraries directories
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.
to see whether there is help information. If the help information appears, it implies that you have installed FastDMA successfully.
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.
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