1. What is MPTC?

MPTC, which stands for Methylation Perspective Track Creator, is a program that creates a data file as a graph file. The graph file is a binary format designed to store numerical value(s) for each genomic coordinate, e. g. numbers for mapped reads, signals of microarray and so on. Using alignment data exported by BMap, MPTC calculates both number of total reads and number of reads supporting DNA methylation, for each genomic coordinate. Then, it expots these numbers into a graph file.

2. How to use MPTC

When BMap complete mapping of your reads, two text files are produced. The first one contains alignments for uniquely mapped reads, and second one contains summary of mapping for each reads. MPTC uses the former file to create graph file. A typical command to run MPTC is as following.

>MPTC -species human -revision hg19 -track YFN -bisulalign YFN.bisulalign -graph YFN.graph -thread 16  

After completion of the command, a graph file will be created (i.e. "YFN.graph" in the example above ). The file can be used for drawing genome browser tracks, calculation of basic statistics of methylome data (i.e. average read depth, GC dependent biases, average methylation rates, and so forth), and domains using changepoint detection. The contents of graph file created by MPTC can be exported to text files with a program named MethylationExport.

Genome browser track

Command line options for MPTC

Option Value type Descriptions
-species string Specify species name. Use in combination with option "-revision" [exclusively required]
-revision string Specify revision name. Use in combination with option "-species" [exclusively required]
-binseq string Specify path to a binseq file. Mutually exclusive with the combination of options "-species" and "-revision" [exclusively required]
-track string Specify the name of data. [requred]
-graph string Specify the path to output graph file. The base name shoudl be the same with the name of data specified with option "-track". [requred]
-thread integer Specify path to a graph file. Mutually exclusive with the combination of options "-species" and "-revision. Only effective for appending mode." [default=1]
-bisulalign string(s) Specify the paths to bisulalign file(s). Multiple paths can be specified at once. Wild cards are allowed. Multiple usage of this option is also allowed. MPTC can read gzipped bisulalign files without gunzipping them if the extension of the file is ".gz". [requred]

3. How to compile MPTC

MPTC is coded with the C++ library Qt, you can compile and use it on the platforms supported by Qt. The source code is available from here.

Once you correctly install Qt in your system, you can easily compile the source codes. After extraction of the source codes to an appropriate directory, change working directory to the directory and type the following commands.

>qmake MPTC.pro
>make (or nmake for Visual Studio on Windows)

After completion of the commands, you can find an executable file in the directory named "bin" located at the same layer with the directory of the source code.

4. Precompiled executables

For your convenience, executable files are prepared as follows.

Platform compiled (Qt version) Link
Windows, 64-bit (Qt5.1) MPTC-v1.0-win64.zip
Macintosh, 64-bit (Qt5.1) MPTC-v1.0-mac64.gz
Linux CentOS 5 , 64-bit (Qt4.7) MPTC-v1.0-linux-centos64.tar.gz