A demo of HiChIP data analysis

Using the H3K27ac GM12878 cell line as an example, we showcase some downstream analyses to process HiChIP data obtained from the HiChIP pipeline. We investigate the distance distribution between each HiChIP interaction and the GC content distribution of HiChIP loop anchors. We also analyze the cell type specificity of each interaction loop. The demo used in this tutorial can be downloaded in either IPython notebook or R markdown.

Individual steps of the analysis