I am new to Hi-C analysis.I am working with a test data set.can any one give me a clear work flow of Hi-C analysis and also can any one tell me about the maths behind the expected matrix and inter and intra chromosomal maps

<p>HOMER contains a HI-C analysis tutorial: <br />
<a href='http://biowhat.ucsd.edu/homer/interactions/index.html'>http://biowhat.ucsd.edu/homer/interactions/index.html</a> <br />
<a href='http://biowhat.ucsd.edu/homer/interactions/HiCtips.html'>http://biowhat.ucsd.edu/homer/interactions/HiCtips.html</a></p>

<p>A quote:</p>

<blockquote>
  <p>Hi-C is a beast of an assay.  There is a lot of information in each
  run, and the size and complexity of the experiments can stretch the
  limits of your computer too.</p>
</blockquote>
