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/Darevska/daUn.hap1.fa.scf.sizes -q 30 -y /sf/storage/gmo/mirmir/data/Darevska/daUn.hap1.fa.DpnII.juicer.txt -n daUn.hap1 -l 2500000,1000000,500000,250000,100000,50000,25000,10000 -z /sf/storage/gmo/mirmir/data/Darevska/daUn.hap1.fa -o /sf/storage/gmo/mirmir/out/Darevska/DU1 -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                      
Sequenced Read Pairs:  572,282,981
 Normal Paired: 376,519,247 (65.79%)
 Chimeric Paired: 30,287,975 (5.29%)
 Chimeric Ambiguous: 13,573,035 (2.37%)
 Unmapped: 151,902,724 (26.54%)
 Ligation Motif Present: 46,464,528 (8.12%)
Alignable (Normal+Chimeric Paired): 406,807,222 (71.08%)
Unique Reads: 26,842,343 (4.69%)
PCR Duplicates: 379,696,799 (66.35%)
Optical Duplicates: 268,080 (0.05%)
Library Complexity Estimate: 26,842,350
Intra-fragment Reads: 2,507,475 (0.44% / 9.34%)
Below MAPQ Threshold: 19,936,111 (3.48% / 74.27%)
Hi-C Contacts: 6,906,232 (1.21% / 25.73%)
 Ligation Motif Present: 442,752  (0.08% / 1.65%)
 3' Bias (Long Range): 51% - 49%
 Pair Type intra chrom %(L-I-O-R): 4% - 87% - 5% - 4%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 68%
 Cis/all (FF and RR orient): 36.8%
Inter-chromosomal: 1,375,934  (0.24% / 5.13%)
Intra-chromosomal: 5,530,298  (0.97% / 20.60%)
Short Range (<20,000bp): 5,030,731  (0.88% / 18.74%)
Long Range (>20,000bp): 499,567  (0.09% / 1.86%)