SuperRec

A fast and accurate 3D chromosomal reconstruction using chromosomal contact information, e.g. Hi-C dataset.

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Please refer our manual for detail usage!

Requirement: Linux
The tool was built statically on a Ubuntu 15.04 laptop. It is self-contained and can run on most 64-bit Linux operation systems like Ubuntu and CentOS without any dynamic library.

Sample Dataset:
(1) In silico chromosomes and Helix structure
(2) real Hi-C dataset


We are glad to share our source code: please send email to shuaicli@cityu.edu.hk to get a copy!

We take sparse contact matrix as input, there are three values in each line (first loci number, second loci number, contact frequency). The loci number should be integer value. If you have a dataset with n loci in dense contact map format (i.e. n*n matrix), you can use the simple script matrix2list.py to convert it into sparse format. python matrix2list.py yourdata.txt > list


example
0 100  43.0
0 22  36.0
0 21  54.0
0 23  34.0
0 24  37.0
0 25  70.0
0 26  36.0
0 27  43.0
0 29  47.0
0 31  46.0
0 33  46.0
0 41  44.0
0 50  38.0
0 27  33.0
0 1 89.0
0 12  38.0
0 11  38.0
0 10  44.0

Output: A list of 3D coordinates in plain text.
For a structure with 100 loci, there should be 100 lines, and on the i-th line, there are three values corresponding the 3D coordinates of the i-th loci.

example

1.178  1.796  0.474
0.903  1.428  0.973
1.432  1.557  1.191
1.078  1.864  0.881
0.554  1.608  1.221
1.053  1.971  1.347
0.932  2.314  1.671
1.322  2.542  1.249
1.461  2.591  0.687
0.987  2.935  0.819
0.723  3.341  0.621
0.571  2.932  0.338
1.012  3.344  0.306


visualization:
You can use the provided script marker.py to plot the structure with python. It plots the structures with line plot function in python package matplotlib.
You may try to use pymol for advanced plot.