Fig. 1

Matrix generation and binning process. a From left to right: (i) the input data to be processed, and paired-end reads to be mapped onto the Ectocarpus. sp. reference v1 genome assembly; (ii) raw contact map before binning—each pixel is a contact count between two restriction fragments (RF); and (iii) raw contact map after binning—each pixel is a contact between a determined number of RFs (see b). b Schematic description of one iteration of the binning process over 10 restriction fragments (arrows). From left to right: (i) initial contact map, each pixel is a contact count between two RFs; (ii) filtering step—RFs either too short or presenting a read coverage below one standard deviation below the mean are discarded; (iii) binning step (1 bin = 3RFs)—adjacent RFs are pooled by three, with sum-pooling along all pixels in a 3 × 3 square; and (iv) binning step (1 bin = 9 RFs)—adjacent RFs are pooled by nine