A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2018-07-13, 18:18 based on data in:
/home/nservant/GIT/MultiQC_TestData/data/modules/hicpro/hicpro-hic
General Statistics
Showing 2/2 rows and 3/11 columns.| Sample Name | M Valid Pairs Unique | Reported Read Pairs | Total |
|---|---|---|---|
| dixon_2M | 0.1 | 0.2 | 0.2 |
| dixon_2M_2 | 0.1 | 0.2 | 0.2 |
HiC-Pro
HiC-Pro is an efficient and flexible pipeline for Hi-C data processing. The MultiQC module is supported since HiC-Pro v2.11.0.
Read Mapping
Alignment of reads in single-end mode.
HiC-Pro uses a two steps mapping strategy. End-to-end mapping is first performed (Full reads Alignments). Unmapped reads are then trimmed at their ligation site, and the 5' end is re-aligned on the reference genome (Trimmed Reads Alignments)
Read Pairing
Pairing of single-end mapping.
HiC-Pro combines aligned reads as pairs. Singleton, low quality pairs or pairs involving multi-mapped reads are usually discarded. Note that the filtering at pairing level can change accrding to the parameters used.
Read Pair Filtering
Filtering of read pairs.
Aligned read pairs are filtered to select valid 3C products from two different restriction fragments. Read pairs coming from the same fragments, such as self-ligation or unligated (danging-end) fragments, are discarded. Ligation products involving neighboring restriction fragment (religation) are also discarded. Finaly, as the ligation should be a random process, valid read pairs from all orientations (R=Reverse, F=forward) are expected to be observed at the same proportion.
Contact Statistics
Contacts statistics after duplicates removal.
Description of contact frequency after duplicates removal. Intra-chromosomal (cis) interaction are expected to be more frequent than inter-chromosomal contacts (trans)
