## [1] "test_dataset1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
99,742 |
99,742 |
| Not Truncated |
92,512 |
92,628 |
| Truncated |
7,230 |
7,114 |
Truncated Read Length
| Average Length Truncated |
22.4 |
22.6 |
Mapping Efficiency
| Too Short To Map |
2,658 |
2,476 |
| Unique Alignments |
73,518 |
72,228 |
| Multiple Alignments |
17,978 |
18,694 |
| Failed To Align |
5,588 |
6,344 |
| Paired |
57,838 |
57,838 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
30,495 |
| Invalid Pairs |
27,343 |
| Same Circularised |
484 |
| Same Dangling Ends |
2,436 |
| Same Fragment Internal |
13,470 |
| Re Ligation |
1,339 |
| Contiguous Sequence |
63 |
| Wrong Size |
9,551 |
| Total Pairs |
57,838 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
30,495 |
30,491 |
| Cis-close (<10Kbp) |
1,399 |
1,399 |
| Cis-far (>10Kbp) |
15,258 |
15,257 |
| Trans |
13,838 |
13,835 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
