Sequenced Read Pairs: 484,493,424
Normal Paired: 190,007,817 (39.22%)
Chimeric Paired: 186,242,031 (38.44%)
Collisions: 12,301,495 (2.54%)
Low MAPQ Collisions: 5,908,629 (1.22%)
Unmapped: 1,950,479 (0.40%)
MAPQ 0: 88,082,973 (18.18%)
Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 376,249,848 (77.66%)
Unique Reads: 258,163,483 (53.29%)
PCR Duplicates: 84,090,529 (17.36%)
Optical Duplicates: 33,995,836 (7.02%)
Library Complexity Estimate: 577,006,879
Intra-fragment Reads: 0 (0.00% / 0.00%)
Hi-C Contacts: 220,114,859 (45.43% / 85.26%)
Ligation Motif Present: 0 (0.00% / 0.00%)
3' Bias (Long Range): 50% - 50%
Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 127,856,830 (26.39% / 49.53%)
Intra-chromosomal: 92,258,029 (19.04% / 35.74%)
Short Range (<20Kb): 56,423,024 (11.65% / 21.86%)
Long Range (>20Kb): 35,824,869 (7.39% / 13.88%)
2026.01.08.22.50.13.HiCImage.pdf
I can see Intra-chromosomal interactions are less. We expect to see much more than this.
we expect to see we expect to see ~20% or fewer Inter-chromosomal interactions. Is there any issue with HIC library preparation? also attached HIC contact map for inter_30.hic.
Sequenced Read Pairs: 484,493,424
Normal Paired: 190,007,817 (39.22%)
Chimeric Paired: 186,242,031 (38.44%)
Collisions: 12,301,495 (2.54%)
Low MAPQ Collisions: 5,908,629 (1.22%)
Unmapped: 1,950,479 (0.40%)
MAPQ 0: 88,082,973 (18.18%)
Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 376,249,848 (77.66%)
Unique Reads: 258,163,483 (53.29%)
PCR Duplicates: 84,090,529 (17.36%)
Optical Duplicates: 33,995,836 (7.02%)
Library Complexity Estimate: 577,006,879
Intra-fragment Reads: 0 (0.00% / 0.00%)
Hi-C Contacts: 220,114,859 (45.43% / 85.26%)
Ligation Motif Present: 0 (0.00% / 0.00%)
3' Bias (Long Range): 50% - 50%
Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 127,856,830 (26.39% / 49.53%)
Intra-chromosomal: 92,258,029 (19.04% / 35.74%)
Short Range (<20Kb): 56,423,024 (11.65% / 21.86%)
Long Range (>20Kb): 35,824,869 (7.39% / 13.88%)
2026.01.08.22.50.13.HiCImage.pdf
I can see Intra-chromosomal interactions are less. We expect to see much more than this.
we expect to see we expect to see ~20% or fewer Inter-chromosomal interactions. Is there any issue with HIC library preparation? also attached HIC contact map for inter_30.hic.