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View Code? Open in Web Editor NEWThe final scripts of my master thesis
The final scripts of my master thesis
# The process detail of my cnn model 1. Download the TSS pair data from the Supplementary Data Set of published paper. Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., & Lis, J. T. (2014). Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genetics, 46(12), 1311โ1320. https://doi.org/10.1038/ng.3142 File name : 41588_2014_BFng3142_MOESM78_ESM 2. Download active promoters and strong enhancers annotation bed files from ChromHMM for K562 cell and GM12878 cell. Websites: http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHmm File name : wgEncodeBroadHmmGm12878HMM.bed, wgEncodeBroadHmmK562HMM.bed 3. Extract active promoters and strong enhancers information from ChromHMM annotation file. grep '255,0,0' wgEncodeBroadHmmGm12878HMM.bed > GM12878_ActivePromoters.bed grep '250,202,0' wgEncodeBroadHmmGm12878HMM.bed > GM12878_StrongEnhancers.bed grep '250,202,0' wgEncodeBroadHmmK562HMM.bed > K562_StrongEnhancers.bed grep '255,0,0' wgEncodeBroadHmmK562HMM.bed > K562_ActivePromoters.bed 4
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