Chromatin Conformation deep analysis
CCdeep can process the data based on several factors:
· filters out sequences with low quality, based on their distant mapping from the selected restriction enzyme site or their attachment to regions with low mappability
· produces an enumeration and quantification (raw and normalized) of pairs of fragment ends
· summarizes the visualization of the biased quantification (GC content, fragment length and mappability)
Detailed instructions on how to install and use the CCdeep utility on your Mac are available HERE.
CCdeep is cross-platform and it works on Mac OS X and Linux. Binaries for the Linux platform are available on the project's homepage.