bedpetools

• A collection of bedpe file operations for HiC-like, or HiChIP data analysis.
• This tool uses pairtools and bedtools.
• This tool implments some functions@[pairtools], which consider pair format different from bedpe format used in some functions such as pairToBed and pairToPair @[bedtools].
• This tool implements some new algorithms using the above tools.
• We have applied bedpetools algorithms to cluster and visualize HiChIP data peak3D.

Bedpe and bedpeGraph formats

• read http://genome.ucsc.edu/FAQ/FAQformat#format1
• we define bedpeGraph when bedpe's 7th column represents numeric values

Selected functions

bedpe-cluster