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.r4 -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.r4 -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 -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                                                
Sequenced Read Pairs:  294,623
 Normal Paired: 171,763 (58.30%)
 Chimeric Paired: 101,557 (34.47%)
 Chimeric Ambiguous: 18,228 (6.19%)
 Unmapped: 3,075 (1.04%)
 Ligation Motif Present: 194,617 (66.06%)
Alignable (Normal+Chimeric Paired): 273,320 (92.77%)
Unique Reads: 266,351 (90.40%)
PCR Duplicates: 1,473 (0.50%)
Optical Duplicates: 5,496 (1.87%)
Library Complexity Estimate: 24,258,808
Intra-fragment Reads: 217,085 (73.68% / 81.50%)
Below MAPQ Threshold: 13,287 (4.51% / 4.99%)
Hi-C Contacts: 253,064 (85.89% / 95.01%)
 Ligation Motif Present: 150,452  (51.07% / 56.49%)
 3' Bias (Long Range): 51% - 49%
 Pair Type intra chrom %(L-I-O-R): 7% - 79% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 61%
 Cis/all (FF and RR orient): 63.1%
Inter-chromosomal: 35,979  (12.21% / 13.51%)
Intra-chromosomal: 217,085  (73.68% / 81.50%)
Short Range (<20,000bp): 171,655  (58.26% / 64.45%)
Long Range (>20,000bp): 45,430  (15.42% / 17.06%)