5C experiment data analysis

[wilson90]

Dear all,

I am going to analyze 5C experiment data, but I have no idea how to go about doing it. Can anyone kindly offer your advice on this?

1. Alignment. (I have read on papers that suggested novoalign from novocraft, but I want to know if there are any other options for alignment)

2. Peak Calling. (Can I use the same peak-calling algorithm in ChIP-Seq?)

3. Interaction file (How to count or visualize the interaction?)

4. any other analysis?

Thank you.

Wilson

[wilson90]

Addition

You can assume that I am proficient in programming.