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>You're essentially asking "can someone tell me everything I need to do and why", while also not saying what you are aiming to do with this data.</p>

<p>Have you read the key papers? Yaffe and Tanay (2011), Lieberman Aiden <em>et al.</em> (2009), Dixon <em>et al.</em> (2012)? The supplementary of Dixon <em>et al.</em> is quite detailed. There's also a decent quick tutorial hosted at BioConductor (<a href="http://www.bioconductor.org/help/course-materials/2011/CSAMA/Friday/Afternoon%20Labs/LiebermanAidenHiC2009.pdf">pdf</a>, <a href="http://www.bioconductor.org/help/course-materials/2011/CSAMA/Friday/Afternoon%20Labs/LiebermanAidenHiC2009.R">R</a>)  that walks you through extracting PC eigenvectors from Lieberman's intrachromosomal data and getting some matching chromatin features.</p>
