Fig. 1

Overview of Hi-C analysis pipelines. These pipelines start from raw reads and produce raw and normalized contact maps for further interpretation. The colored boxes represent alternative ways to accomplish a given step in the pipeline. RE, restriction enzyme. At each step, commonly used file formats (‘.fq’, ‘.bam’, and ‘.txt’) are indicated. a, The blue, pink and green boxes correspond to pre-truncation, iterative mapping and allowing split alignments, respectively. b, Several filters are applied to individual reads. c, The blue and pink boxes correspond to strand filters and distance filters, respectively. d, Three alternative methods for normalization