1. What is CalcCoverage?

CalcCoverage is a program that calculate basic statistics of DNA methylome data. It report depth of reads, methylation rates and so on. This program is intended for use with whole-genome bisulfite sequencing (WGBS) data. For target bisulfite sequencing (TBS), you may have interested in CalcEnrichment.

2. How to use CalcCoverage

CalcCoverage uses graph file for its calculation. So, before using CalcCoverage,  you have to prepare graph file with MPTC.

A typical command is as following.

>CalcCoverage -graph YFN.graph -out YFN.html

After completion of the command, a file reporting basic statistics of methylome data will appear (i.e. "YFN.html" in the example above ).

Command line options for CalcCoverage

Option Value type Descriptions
-graph string Specify the path to graph file. There are some programs that can create graph file(s), CalcCoverage accept only graph files created by MPTC. [requred]
-out string Specify the paths to output file. If the path contains an extension "html",  output of CalcCoverage becomes graphical one. [requred]

3. How to compile CalcCoverage

CalcCoverage 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 CalcCoverage.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. A Notice for running CalcCoverage in graphical mode

In some platforms, CalcCoverage uses functions provided by an open source library QCustomPlot in graphical html output mode. Since  QCustomPlot requires X-window system, CalcCoverage needs both a launched X-server process and a correct environment variable "DISPLAY". If CalcCoverage can not find X-window system, an error message like following will appear.

>CalcCoverage : cannot connect to X server localhost:10.0

To solve this, we use virtual X11 display server Xvfb. After installing Xvfb appropreately, we type following command to launch Xvfb.

>Xvfb :1 -screen 0 1024x768x24 1>/dev/null 2>/dev/null &

Then set an environment variable "DISPLAY" with typing following command.

>export DISPLAY=:1.0

After completion of runnning CalcCoverage, the Xvfb process can be killed as following.

>kill Xvfb

5. Precompiled executables

For your convenience, executable files are prepared as follows.

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