ChIPSeq Analysis

Raw Data

Input formats and experiment type: FASTQ, single-end.

These files are a subset of public available SRR402848: GATA-1 ChIPseq and SRR402850: Input sample from Wontakal SN, Guo X, Smith C, MacCarthy T et al. A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proc Natl Acad Sci USA 2012 Mar 6;109(10):3832-7 doi: 10.1073/pnas.1121019109

  • Reads length: 36

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 ChIPSeq test data.
  3. Open a terminal

Decompress

tar xvfz ChIPSeqTestData.tgz
cd YOUR_TEST_PATH/ChIPSeqTestData/reference

Execute BWA indexing:

YOUR_BWA_PATH/bwa index -a bwtsw mm9.chr10.fa

Configure experiment XML file:

YOUR_TEST_PATH/ChIPSeqTestData/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_v3.7/ChIPseq/config/configProgramPaths.xml.
You can modify the file using a text editor or RubioSeq+GUI

RUN RUbioSeq:

Console execution
PathToRUbioSeq/RUbioSeq.pl --analysis ChIPseq --config YOUR_TEST_PATH/ChIPSeqTestData/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

Final results with peaks are available at PROJECT_DIRECTORY/Experiment1/sharp_peaks/