HiCNAtra pipeline and RD signal computation. a Block diagram of the HiCNAtra software showing different computational modules. b Schematic illustration of the RD signal computation methods using Hi-C (left) and 3C-seq (right) reads. Left: For Hi-C data, informative and non-informative (only dangling-end reads are shown) reads (top panel) mapped within the restriction fragment-end windows (second panel) are used for RD calculation. Then, the number of reads is counted for each window (third panel). Base counts are then estimated for each restriction fragment as the summation of the counts of its two fragment-end windows (bottom panel). Right: For 3C-seq data (top panel), genomic reads (middle panel) are exclusively used to compute the RD signal in an unbiased manner similar to WGS paired-end reads (bottom panel)
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