Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 4 threads; /home/mirmir/work/progs/juicer-master/CPU/juicer.sh: line 338: java: command not found; /home/mirmir/work/progs/juicer-master/CPU/juicer.sh -t 4 -d /home/mirmir/work/fastq/Darevska/DU1 -p /sf/storage/gmo/mirmir/data/hg38/hg38.fa.scf.sizes -q 30 -y /sf/storage/gmo/mirmir/data/hg38/hg38.fa.DpnII.juicer.txt -n hg38 -l 2500000,1000000,500000,250000,100000,50000,25000,10000 -z /sf/storage/gmo/mirmir/data/hg38/hg38.fa -o /sf/storage/gmo/mirmir/out/hg38/DU1 -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                                                          
Sequenced Read Pairs:  572,282,981
 Normal Paired: 10,981,981 (1.92%)
 Chimeric Paired: 769,573 (0.13%)
 Chimeric Ambiguous: 742,047 (0.13%)
 Unmapped: 559,789,380 (97.82%)
 Ligation Motif Present: 46,464,528 (8.12%)
Alignable (Normal+Chimeric Paired): 11,751,554 (2.05%)
Unique Reads: 3,171,329 (0.55%)
PCR Duplicates: 8,539,127 (1.49%)
Optical Duplicates: 41,098 (0.01%)
Library Complexity Estimate: 3,261,265
Intra-fragment Reads: 355,879 (0.06% / 11.22%)
Below MAPQ Threshold: 1,469,074 (0.26% / 46.32%)
Hi-C Contacts: 1,702,255 (0.30% / 53.68%)
 Ligation Motif Present: 591,295  (0.10% / 18.65%)
 3' Bias (Long Range): 62% - 38%
 Pair Type intra chrom %(L-I-O-R): 11% - 67% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 46%
 Cis/all (FF and RR orient): 64.0%
Inter-chromosomal: 333,294  (0.06% / 10.51%)
Intra-chromosomal: 1,368,961  (0.24% / 43.17%)
Short Range (<20,000bp): 924,026  (0.16% / 29.14%)
Long Range (>20,000bp): 444,935  (0.08% / 14.03%)