HiCExplorer QC report
Pairs considered
Pairs used & filtered
This figure contains the number of reads that were finally used to build the Hi-C matrix along with the reads that where filtered out.
- Dangling ends
- These are reads that start with the restriction site and constitute reads that were digested but no ligated.
- Same fragment
- These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between. These read pairs are not valid Hi-C pairs
- Self circle
- self circles are defined as pairs within 25kb with 'outward' read orientation
- Self ligation
- These are read pairs with a restriction site in between that are within 800 bp.
Contact distance
Read orientation
