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This article will explain in detail about the use of HiCPlotter tools, the editor thinks it is very practical, so share it for you to do a reference, I hope you can get something after reading this article.

HiCPlotter is a command-line tool used to demonstrate the interaction matrix of Hi-C. In addition to the basic use of heat maps to show the interaction matrix, it also supports the addition of annotation information for two-dimensional data such as gene structure, chip_seq and so on.

Https://github.com/kcakdemir/HiCPlotter

For interaction matrices, multiple formats are supported

1. General format

The Hi-C interaction matrix is in bin units, each row and column represent a bin, and the values of the corresponding cells reflect the frequency of interaction between the two bin. The common format is as follows

Bin1 Bin2 Bin3 Bin4 Bin5 Bin6

7.85957 4.80329 11.4766 9.57416 4.5288 8.55022

8.61621 4.98956 2.35654 5.69483 11.1187 10.1322

4.06803 4.07801 7.98047 2.59144 6.3851 7.74306

4.52869 2.70624 8.94544 4.29185 8.29491 8.38257

The line at the beginning of # and the first line are treated as comment messages and are ignored.

2. HiC-Pro proprietary format

In order to solve the problem that the traditional interaction matrix is too large, HiC-Pro has specially developed a new format, as shown below

1050 1586 1

1050 1589 1

1050 1590 1 (jumps to 1612)

1050 1612 2

A total of three columns, the first two columns correspond to the number of bin, the number of the third column represents the frequency of interaction between the two bin, there is no interaction between the bin will not be recorded in the file. In addition to this file, the following files are required

Chr1 20960000 20980000 1049

Chr1 20980000 21000000 1050

Chr1 21000000 21020000 1051

Chr1 21020000 21040000 1052

Chr1 21040000 21060000 1053

Chr1 21060000 21080000 1054

Chr1 21080000 21100000 1055

The chromatin location corresponding to each bin number is given, and the chromatin interaction information can be described completely through these two files.

The basic usage of the software is as follows

Python,\

HiCPlotter.py\

-f matrix.txt\

-n hES\

-chr chr21\

-r 40000\

-o default1\

The-f parameter specifies the input Hi-C interaction matrix,-n specifies the title name of the interaction matrix heat map,-chr specifies the name of the chromatin to be drawn,-r specifies the corresponding resolution, and-o specifies the prefix of the output file. The result is as follows

For the output format of HiC-Pro, the usage is as follows

Python\

HiCPlotter.py\

-f matrix.txt\

-tri 1\

-bed bin.bed\

-chr chr7\

-o Example\

-r 40000\

-n hES

-tri 1 declares that the format of the input interaction matrix is the output format of HiC-Pro,-bed specifies the chromatin location file corresponding to the bin number, and other parameters are the same as the basic usage.

The software supports simultaneous visualization of multiple interaction matrices, which can be used as follows

Python\

HiCPlotter.py\

-f matrix1.txt matrix2.txt matrix3.txt\

-n name1 name2 name3\

-chr chr6\

-r 40000\

-o example

The corresponding-f and-n parameters are multiple parameters separated by spaces, and the results are as follows

In addition to the above basic usage, you can also add annotation information, such as gene structure, corresponding chip_seq data, and so on. The results are shown below.

At this point, you need to enter files corresponding to various comments. For different comments, different formats are required. For more details, please refer to the official documentation.

This is the end of this article on "what is the use of HiCPlotter tools". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, please share it for more people to see.

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