Standalone QBioDiff
The standalone QBioDiff is provided to facilitate user to preprocess the data by Next Generation Sequencing technologies such as ChIP-Seq, RNA-Seq et al. The standalone QBioDiff can calculate the read numbers in the ROIs provided by user and then normalize the counted number by region length. The normalized read numbers in ROIs are used for further quantitative analysis on the QBioDiff web server.
Firstly, Download the Standalone QBioDiff to your own computer.

Then, Run the Standalone QBioDiff in the command line terminal using command:
java -jar -Xmx2048m Standalone_QBioDiff.jar -R RegionFile=/example.bed,ReadFolder=/ReadFile,ResultFolder=/Result,ExpandLength=200,BinSize=1,DepthNormalization=NO

-Xmx1024m: Use maximum memory for 1024M.
RegionFile: the file path for the import region data (File format should be bed).
ReadFolder: the folder path including the raw read files of biological data by ChIP-Seq or RNA-Seq (Read file format should be bed).
ResultFolder: the folder path for the export of analysis results of Standalone QBioDiff.
Expand Length: Applicable to the single-terminal sequencing data. User can select or input the suitable length
of sequence represented by each read. Each read is expanded to the length firstly, and then mapped to corresponding
region.
Bin Size: the unit of region segment. The default value is 1 bp meaning the total read number in each region is
normalized by the region length.
Depth Normalization: (YES or NO,YES--In Depth Normalization,NO--Don't Depth Normalization)Considering the different sequencing depth of raw data files, the read number is further
normalized by the total read number of the given raw data file relative to the mean of the total read numbers
of the all used raw data files.

In the end, Upload the result file formatted in gct to QBioDiff web server for further analysis.
 
Note:
A example data profiled by ChIP-seq for Standalone_QBioDiff is provided for user to try Standalone_QBioDiff on your own computer.
User can use this example to try out the Standalone QBioDiffto pretreat the data by Next Generation Sequencing technologies such as ChIP-Seq, RNA-Seq et al.
This example is the data of 39 histone modifications, CTCF, H2AZ and PolII profiled by ChIP-Seq in CD4 T cells.
Example Region File Example_Region_hg18_CpGisland.bed
Example ChIP-Seq File Example_ChIPSeq_hg18_Histonemodification_CD4.zip
Try Standalone QBioDiff as following:
1. Download these two data.
2. Unzip the file Example_ChIPSeq_hg18_Histonemodification_CD4.zip.
3. Run the Standalone QBioDiff in the command line terminal using command:
java -jar -Xmx2048m Standalone_QBioDiff.jar -R RegionFile=/Example_Region_hg18_CpGisland.bed,ReadFolder=/Lymph,ResultFolder=/Result,ExpandLength=200,BinSize=1,DepthNormalization=NO