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
- 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 here. Note: If you want to execute the quickTest with RubioSeq+GUI, follow the manual to launch and configure the graphical interface.
- Download ChIPSeq test data.
- Open a terminal
Execute BWA indexing:
Configure experiment XML file:
You can modify the file using a text editor or RubioSeq+GUI
Configure programs XML file located at:
PathToRUbioSeq/RUbioSeq.pl --analysis ChIPseq --config YOUR_TEST_PATH/ChIPSeqTestData/experimentTest.xml
Click "Execute experiment" button, select the file and run. See for further information
Final results with peaks are available at PROJECT_DIRECTORY/Experiment1/sharp_peaks/