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This article mainly explains "how to use TADbit to identify topology association domains". The content of the explanation is simple and clear, and it is easy to learn and understand. Please follow the editor's train of thought to study and learn "how to use TADbit to identify topology association domains".

TADbit is a hi-c data analysis software that provides complete functions from raw data processing to chromatin 3D modeling. The corresponding article links are as follows

Https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540598/

The pipeline of the software is shown in the following figure

It is divided into the following three functional modules

FASTQ

Interacton Matrix

3D Models

The first module starts from the original fastq file, carries on the quality filter to the sequence, uses the GEM software to compare the clean reads to the reference genome, then carries on the screening, constructs the original interaction matrix, and carries on the normalization processing to get the normalized interaction matrix.

The second module is used to visualize the hi-c interaction matrix, and on the basis of the interaction matrix, the TAD topology association domain can be identified, and the TAD can be visualized and clustered.

The third module is used to construct the model of three-dimensional conformation of chromatin and analyze the structure.

This article briefly sorts out the specific usage of the second module, and the detailed steps are as follows

1. Visual hi-c matrix

The software is developed with python and object-oriented programming ideas. the first thing to do is to build an object. The corresponding hi-c interaction matrix is needed in the construction process. The test data set of the software contains the following two hi-c matrices.

HIC_gm06690_chr19_chr19_100000_obs.txt

HIC_k562_chr19_chr19_100000_obs.txt

Corresponding to the interaction matrix under the resolution of chromosome 19 100kb of GM06690 and K562 cell lines. The code for building objects based on these two interaction matrices and visualizing them is as follows

The visual effect is as follows

two。 Predict and visualize TAD domains

There are two visualization strategies, the first is to mark the TAD area with a rectangle on the heat map of hi-c, and the second is called density plot, which is used as follows

The effect of the heat map marked TAD is as follows

The effect of density plot is as follows

3. TAD Alignment

By comparing the TAD of multiple cells or tissues, we can analyze whether their locations are conservative. The usage is as follows

The effect picture is as follows

The use of TADbit is simple and the visualization is great, but the only drawback is that it takes a lot of effort to install.

Thank you for your reading, the above is the content of "how to use TADbit to identify topology association domains". After the study of this article, I believe you have a deeper understanding of how to use TADbit to identify topology association domains, and the specific use needs to be verified in practice. Here is, the editor will push for you more related knowledge points of the article, welcome to follow!

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