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hicInfo (version 3.7.2+galaxy0)

Get information about you Hi-C matrix

This scripts returns useful information about your Hi-C interaction matrix. However, the following information can be included if it is provided by the Hi-C interaction matrix meta data. In case the meta data is missing, the information can be less.

# Matrix information file. Created with HiCExplorer's hicInfo version 3.2-dev
File:       /tmp/
Date:       2019-08-11T19:46:15.959678
Genome assembly:    dm3
Size:       33,754
Bin_length: 5000
Number of chromosomes:      15
Non-zero elements:  35,857
The following columns are available: ['chrom' 'start' 'end']

Generated by:       HiCMatrix-11-dev
Cooler library version:     cooler-0.8.5
HiCMatrix url:
Interaction matrix created with:    HiCExplorer-3.2-dev

Build statistics:

File        /tmp/
Sequenced reads     99983
Min rest. site distance     300
Max library insert size     1000

#   count   (percentage w.r.t. total sequenced reads)
Pairs mappable, unique and high quality     52726   (52.73)
Hi-C contacts       37321   (37.33)
One mate unmapped   8777    (8.78)
One mate not unique 3603    (3.60)
Low mapping quality 34877   (34.88)

#   count   (percentage w.r.t. mappable, unique and high quality pairs)
dangling end        0       (0.00)
self ligation (removed)     0       (0.00)
One mate not close to rest site     0       (0.00)
same fragment       15393   (29.19)
self circle 0       (0.00)
duplicated pairs    12      (0.02)

#   count   (percentage w.r.t. total valid pairs used)
inter chromosomal   5955    (15.96)
Intra short range (< 20kb)  8853    (23.72)
Intra long range (>= 20kb)  22513   (60.32)
Read pair type: inward pairs        7145    (19.14)
Read pair type: outward pairs       9731    (26.07)
Read pair type: left pairs  7156    (19.17)
Read pair type: right pairs 7334    (19.65)

Please have in mind that the provided information depends on the tool and its version with which the matrix was created.

For more information about HiCExplorer please consider our documentation on