Welcome to the EpiChIP website


Daniel Hebenstreit1, Muxin Gu1, Syed Haider2, Daniel Turner3, Pietro Lio2, Sarah Teichmann1
1 Laboratory of Molecular Biology, Medical Research Council, 2 Computer Laboratory, University of Cambridge, 3 Wellcome Trust Sanger Institute


What's the system requirement?
Java 1.6 or above
You can check your java version by typing "java -version" under command line.
Free space: twice of your input read file's effective size. (Typically 500 MB is enough);
How to change Java version to 1.6 on MAC OS?
Go to Applications -> Utilities -> Java Preferences. Under the "General" tab, uncheck any version apart from Java 1.6 (or Java 6).
Does it matter which platform I'm using.
No. It works on Java Runtime Environment which is platform-independent.





What analyses does EpiChIP do?
Find out how many bases fall into each gene (Gene Scoring);
    Visualise the distribution of gene scores;
    Separate bimodal distribution (Curve Fitting);
    Study the correlation with another data set (Correlation);
Line up and view the read distribution across all genes, exons or introns (Window Analysis);
    Visualise the read distribution;
    Find windows and rank windows (Window Finding);
Compare Experiment with Control;
What are the requirements for the input read file?
BED file (1 based) from UCSC Genome Browser and the output of Maq, Bowtie and Eland are guaranteed to work.
How to analyse paired-end sequencing?
You will have to pre-process the reads into a BED file where each line represents a read and the 2nd and 3rd column marks the lower and higher boundary of the read respectively.
How to format the gene expression data for correlation plot?
The gene expression data must contain one column for gene names and one for the LOG values of gene expression.
However the file could have more columns. The software will ask the user to specify the two columns above.





How are the histone modification values normalised? What is NLCS?
The normalised value (NLCS) is the number of bases (nucleotides) of sequencing reads within the window normalised to every million reads. One can directly compare the NLCS values of the same window but the NLCS calculated from different windows or data sets may not be directly compared.






I have questions about EpiChIP. Where do I find help?
If you are not sure how to use EpiChIP, here is the tutorial.
If you have questions about the technical details, you may refer to the documentation.
For specific questions regarding to the software, you may click the Help button to view the help on the specific feature of the software.

Funding: The project is funded by Medical Research Council