Copy Number Variation Analysis

Raw Data

Input formats and experiment type: BAM, .txt (baseline file), single-end.

These files are publicly available at CONTRA web site. Download.

  • Reads number: 10230604
  • Reads length: 75

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 CNV test data.
  3. Open a terminal

Decompress

tar xvfz CNVTestData.tgz
unxz YOUR_TEST_PATH/CNVTestData/reference/*.xz
unxz YOUR_TEST_PATH/CNVTestData/reference/base/*.xz

Configure experiment XML file:

YOUR_TEST_PATH/CNVTestData/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 at:

INSTALLATION_PATH/RUbioSeq_v3.2.1/variantCalling/config/cnv/configProgramPaths.xml.
You can modify the file using a text editor or RubioSeq+GUI

RUN RUbioSeq:

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