The matrix format is the standard input for the HiCRep reproducibility analysis. It has the dimension of N*(3+N). The additional first three columns are chromosome name, and mid-point coordinates of two contacting bins. The converted format has three columns. The first two columns are mid-point coordinates of two contacting bins, and the third column is the reads number in each bin.
a Hi-C intra-chromosome matrix in the format of N*N (No chromsome name and coordinates columns).
a vectorized Hi-C data. The first two columns are mid-point coordinates of the two contacting bins. The third column is read numbers of the contacts.
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. bioRxiv 101386; doi: https://doi.org/10.1101/101386.
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