Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 8 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 8 -d /home/mirmir/work/fastq/Darevska/DV1 -p /sf/storage/gmo/mirmir/data/Darevska/daVa.2.fa.scf.sizes -q 30 -y /sf/storage/gmo/mirmir/data/Darevska/daVa.2.fa.DpnII.juicer.txt -n daVa.2 -l 2500000,1000000,500000,250000,100000,50000,25000,10000 -z /sf/storage/gmo/mirmir/data/Darevska/daVa.2.fa -o /sf/storage/gmo/mirmir/out/DV1.plus -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                                      
Sequenced Read Pairs:  276,618,087
 Normal Paired: 234,593,533 (84.81%)
 Chimeric Paired: 13,621,960 (4.92%)
 Chimeric Ambiguous: 5,432,403 (1.96%)
 Unmapped: 22,970,191 (8.30%)
 Ligation Motif Present: 13,062,462 (4.72%)
Alignable (Normal+Chimeric Paired): 248,215,493 (89.73%)
Unique Reads: 123,858,703 (44.78%)
PCR Duplicates: 121,736,912 (44.01%)
Optical Duplicates: 2,619,878 (0.95%)
Library Complexity Estimate: 156,372,210
Intra-fragment Reads: 33,125,633 (11.98% / 26.74%)
Below MAPQ Threshold: 44,078,610 (15.93% / 35.59%)
Hi-C Contacts: 79,780,093 (28.84% / 64.41%)
 Ligation Motif Present: 2,953,314  (1.07% / 2.38%)
 3' Bias (Long Range): 50% - 50%
 Pair Type intra chrom %(L-I-O-R): 1% - 96% - 2% - 1%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 84%
 Cis/all (FF and RR orient): 23.4%
Inter-chromosomal: 10,060,154  (3.64% / 8.12%)
Intra-chromosomal: 69,719,939  (25.20% / 56.29%)
Short Range (<20,000bp): 68,349,985  (24.71% / 55.18%)
Long Range (>20,000bp): 1,369,954  (0.50% / 1.11%)