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What is the use of the Juicebox tool

2025-01-28 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >

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Editor to share with you what the use of Juicebox tools, I believe that most people do not know much about it, so share this article for your reference, I hope you will learn a lot after reading this article, let's go to understand it!

After running the Juicer software, you will get a result file with the suffix hic, which can be imported into the tool juicebox for visualization. This tool is a graphical interface tool that can easily view and display Hi-C atlas. You can download the software from the link below.

Https://github.com/aidenlab/juicebox/wiki/Download

The GUI tool developed in Java language supports multiple platforms. The interface after startup is as follows

Use File- > open to import files with the suffix hic for viewing, you can import local files, or you can enter url. The software also has a built-in ENCODE dataset, as shown below

Double-click to import, and the interface after import is as follows

First of all, the HI-C map of all chromosomes is displayed. Through the toolbar, you can select chromatin, adjust the resolution, normalize the interaction matrix, and adjust the displayed chromatin region. Take chromatid 17 as an example, in the Chromosomes column, both columns select chromosome 17, and the rows and columns that represent the interaction matrix are chromosome 17, and then click the refresh button on the right, and the results are as follows

Adjust the normalization method through the Normalization tool; adjust the resolution through the Resolution tool; adjust the displayed chromosome region through the Goto tool.

Hi-C atlas can be viewed and displayed through simple operation. In addition to these basic functions, you can also import comment files. You can open the comment file panel through View- > Show Annotation Panel. The annotation information is divided into 1D and 2D. 1D mainly refers to information such as chip_seq,RNA_seq, 2D refers to TAD, chromatin ring and other information. Through Load ENCODE, you can import one-dimensional comments in the ENCODE database, as shown below.

Check the comment information to be imported, and import it through Load. After entering, the interface is as follows

The color and other configurations of each imported track can be adjusted in the panel, as shown below

2D annotation information can be imported through Load Loops/Domain, as shown below

After import, you can see the corresponding tags in the Hi-C graph, as shown below

Yellow areas are marked with TAD, light blue areas are marked with chromatin rings, and adjusted images can also be exported to PDF or SVG format.

Through juicebox, you can dynamically explore Hi-C atlas and easily achieve high-quality Hi-C image visualization.

These are all the contents of this article entitled "what are Juicebox tools for?" Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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