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/alOe.egs -p /sf/storage/gmo/mirmir/data/alOe/alOe.r10a.agp.chr.sizes -q 30 -y /sf/storage/gmo/mirmir/data/alOe/alOe.r10a.fa.DpnII.juicer.txt -n alOe.egs -l 2500000,1000000,500000,250000,100000,50000,25000,10000 -z /sf/storage/gmo/mirmir/data/alOe/alOe.r10a.fa -o /sf/storage/gmo/mirmir/out/alOe.egs -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                                          
Sequenced Read Pairs:  372,936
 Normal Paired: 251,341 (67.40%)
 Chimeric Paired: 98,361 (26.37%)
 Chimeric Ambiguous: 18,930 (5.08%)
 Unmapped: 4,304 (1.15%)
 Ligation Motif Present: 316,758 (84.94%)
Alignable (Normal+Chimeric Paired): 349,702 (93.77%)
Unique Reads: 340,141 (91.21%)
PCR Duplicates: 2,721 (0.73%)
Optical Duplicates: 6,840 (1.83%)
Library Complexity Estimate: 21,486,874
Intra-fragment Reads: 290,334 (77.85% / 85.36%)
Below MAPQ Threshold: 16,004 (4.29% / 4.71%)
Hi-C Contacts: 324,137 (86.91% / 95.29%)
 Ligation Motif Present: 257,687  (69.10% / 75.76%)
 3' Bias (Long Range): 46% - 54%
 Pair Type intra chrom %(L-I-O-R): 5% - 83% - 6% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 70%
 Cis/all (FF and RR orient): 65.6%
Inter-chromosomal: 33,803  (9.06% / 9.94%)
Intra-chromosomal: 290,334  (77.85% / 85.36%)
Short Range (<20,000bp): 237,392  (63.65% / 69.79%)
Long Range (>20,000bp): 52,942  (14.20% / 15.56%)