Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 6 threads; java version "1.8.0_45"; ./juicer.sh -t 6 -g mm10/ -D /mnt/storage/home/aselsukova/juicer -d /mnt/storage/home/aselsukova/juicer/scratch/mastocytes/VL_A2 -s DpnII -p /mnt/storage/home/aselsukova/juicer/chrom.sizes/chrom.sizes_mm10 -y /mnt/storage/home/aselsukova/juicer/restriction_sites/mm10_DpnII.txt -z /mnt/storage/home/aselsukova/juicer/scratch/juicer_scratch/references/mm10/mm10.fa                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Sequenced Read Pairs:  28,567,242
 Normal Paired: 16,788,459 (58.77%)
 Chimeric Paired: 7,914,199 (27.70%)
 Chimeric Ambiguous: 2,318,496 (8.12%)
 Unmapped: 1,546,088 (5.41%)
 Ligation Motif Present: 13,561,376 (47.47%)
Alignable (Normal+Chimeric Paired): 24,702,658 (86.47%)
java -Djava.awt.headless=true -Xmx16000m -jar /mnt/storage/home/aselsukova/juicer/scripts/common/juicer_tools.jar LibraryComplexity /mnt/storage/home/aselsukova/juicer/scratch/mastocytes/VL_A2/aligned inter.txt
Intra-fragment Reads: 2,647,995 (9.27% / 12.73%)
Below MAPQ Threshold: 3,983,779 (13.95% / 19.16%)
Hi-C Contacts: 14,164,154 (49.58% / 68.11%)
 Ligation Motif Present: 8,160,932  (28.57% / 39.24%)
 3' Bias (Long Range): 77% - 23%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 7,213,830  (25.25% / 34.69%)
Intra-chromosomal: 6,950,324  (24.33% / 33.42%)
Short Range (<20Kb): 2,426,682  (8.49% / 11.67%)
Long Range (>20Kb): 4,523,640  (15.84% / 21.75%)