Fig. 3
From: NaviSE: superenhancer navigator integrating epigenomics signal algebra
Scheme of parallelization of stitching. 1 Determination of the number of processes (k STIT) based on Eq. 4 for a case in which the number of available cores (C) is 10, the maximum number of cores reserved by the user (C u ) is 7, the memory main of the computer (M) is 64 GB, the memory allocated to stitching (m STIT) is 3 GB and the cardinal (l STIT) of the set of chromosomes (D STIT={d 1=1,d 2=2,⋯,d 22=22,d 23=X,d 24=Y}) is 24. The resulting number of allocated cores calculated by Eq. 4 is k STIT=C u =7. 2 Construction of data chunks is calculated by Eq. 5. Since k STIT=7, the set of chromosomes, D STIT, is divided into 7 subsets or chunks: D 1,STIT={d 1,d 8,d 15,d 22}; D 2,STIT={d 2,d 9,d 16,d 23}; ⋯; D 6,STIT={d 6,d 13,d 20} and D 7,STIT={d 7,d 14,d 21}. 3 Assignment of information elements. In the case of stitching, assigned elements are MACS peaks (inferred as enhancers). After the assignment of the subsets D 1,STIT, D 2,STIT, etc., the set of MACS peaks, S STIT={s 1,s 2,⋯ } is divided into 7 subsets of elements, \(S_{D_{1,\text {STIT}}}=\{s_{1}, s_{6}, s_{8},\cdots \}\), \(S_{D_{2,\text {STIT}}}=\{s_{2}, s_{10}, s_{14},\cdots \}\), ⋯, \(S_{D_{7,\text {STIT}}}=\{s_{5},s_{9},s_{12},\cdots \}\), based on the chromosome of each row. Finally, all the subsets of elements are simultaneously processed by NaviSE, combined into one file, and the SE ranks are calculated