Methylation Calling

Raw Data

Input data has been generated with Sherman.
Input format and experiment type: Fastq, Lister, paired-end

  • Reads number: 1000000 per file
  • Reads length: 50
  • Synthetic CpG rate: ~30%
  • Synthetic CHH,CHG rate: ~5%

Steps

  1. Use RUbioSeq's LiveDVD or Download source code and install manually all programs and prerequisites for variant calling analysis especified in RUbioSeq's manual. Most of RUbioSeq's required programs can be downloaded hereNote: If you want to execute the quickTest with RubioSeq+GUI, follow the manual to launch and configure the graphical interface
  2. Download methylation calling test data.
  3. Open a terminal

Decompress

tar xvfz MethylationTestData.tgz

Configure experiment XML file:

YOUR_TEST_PATH/MethylationTestData/experimentTest.xml
You only need to configure the filenames paths to your corresponding directory.
You can modify the file using a text editor or RubioSeq+GUI

Configure programs XML file located in

PathToRUbioSeq/MethylCSeq/MethylBis/config/configProgramPaths.xml
You only need to configure the filenames paths to your corresponding directory.
You can modify the file using a text editor or RubioSeq+GUI

RUN RUbioSeq:

Console execution
PathToRUbioSeq/RUbioSeq.pl --analysis methylationCalling --config YOUR_TEST_PATH/MethylationTestData/experimentTest.xml
GUI execution
Click "Execute experiment" button, select the file and run. See for further information
Please read the manual in order to locate and understand the output files

Results

RUbioSeq calculates the same percentages as we have synthetically generated with Sherman.