| 4 | 4 | The [[https://science.sciencemag.org/content/326/5950/289 | Hi-C method]] Hi-C method generalizes earlier experimental techniques, such as 3C or 5C, for characterizing contacts between specific chromosomal loci, to enable unbiased identification of chromatin interactions across an entire genome. Two software pipelines for analyzing data from Hi-C experiments are [[https://github.com/aidenlab/juicer | juicer]] and [[https://github.com/nservant/HiC-Pro | HiC-Pro]]. An example for using HiC-Pro on Whitehead computing resources with data collected with a kit from Arima Genomics is outlined below. Note that in this example, a reference genome is used that excludes unlocalized or unplaced contigs from the assembly. This choice is taken to ease downstream analysis. Please see the HiC-Pro [[http://nservant.github.io/HiC-Pro/ | documentation]] for additional examples. |
