![]() Let’s take a look at the whole chromosome. This might be useful to explore large regions. We will use the HiCexplorer command line tools for this purpose.įirst, let’s plot a square matrix. Hi C Flashin Fruit Punch Juice Box Contains Pure Filtered Water, Sweeteners (High Fructose Corn Syrup, Sugar), Orange and Pineapple Juices from Concentrate. This is useful for generating reproducible workflows. Detailed documentation is available on the wiki. Download Juicebox here, or use Juicebox on the web. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. HiCexplorer for command line visualizationĪnother visualization approach is to include a command in a script that automatically generates figures. Juicebox is visualization software for Hi-C data. Explore multiple resolutions and corrections.Use HiCExplorer to generate images of a matrix sliceĪ common visualization task for HiC data is to interactively explore the matrix for quality control purposes, to generate hypothesis or to confirm expected interaction patterns.įor the first part of the practical, we are using the juicebox browser interactively.Use other annotations for more in-depth exploration of the results. You can zoom in or scroll around in the heatmap to better understand where the DIRs occur in relation to each other and on the chromatin map. The blue boxes on the heatmap represent the significant DIRs. These.hic files are built from sequenced read pair files from a Hi-C experiment. Here we can see a screenshot of Juicebox with the Rao 2017 data loaded and our annotations visualized on the heatmap. Juicebox uses a complementary software package, Juicer, to build.hic files that store binary contact matrices at different resolutions. These properties are supported in juicebox-notebook, however juicebox-notebook also provides equivalent path properties for specfiying paths to local files when used with Jupyter Notebook or Colab. For the first part of the practical, we are using the juicebox browser interactively. Configuration objects for juicebox.js maps (.hic files) and tracks have properties to specify URLs to files for data and indexes. The DIRs will appear as blue rectangles on the heatmap. Juicebox interactive visualization A common visualization task for HiC data is to interactively explore the matrix for quality control purposes, to generate hypothesis or to confirm expected interaction patterns. Select chromosome 16 in both drop-down menus below the “Chromosomes” selection toolbar and click the refresh button. After loading it, the “rao2017Annotations.txt” annotations will be shown in the “Select 2D annotation file(s) to open” panel - select it and click the Open button to load in into Juicebox. You can also download a full-fledged desktop version of Juicebox. tab/button, and navigate to the “rao2017Annotations.txt” file. Juicebox.js is cloud-based visualization software for Hi-C data created by Jim Robinson and Douglass Turner of the IGV team, in collaboration with Neva C. Alternatively, use the View > Show Annotations Panel menu. Structural features, such as loops and domains, are automatically annotated. This file has been pre-generated, right-click and save it from here.Īssuming the “Rao et al. | Cell 2017” “Auxin treated (6 hrs)” data is loaded, click the Show Annotation Panel button at the lower right corner of Juicebox window. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. This function will create a text file in your working directory containing the annotations which can then be imported into Juicebox. exportJuicebox(rao2017, logfc_cutoff = 2, logcpm_cutoff = 1, p.adj_cutoff = 0.001, file_name = "rao2017Annotations.txt") Say your Hicexp object is named rao2017 simply run the following line of code in R. Each Hi-C box contains a full days supply of vitamin c, is made with real fruit juice and has the great taste your kids love. You will want to select the main map for “Auxin treated (6 hrs)”.Īssuming you have already analyzed the data using multiHiCcompare and you now have a Hicexp object containing the comparison results you can use the exportJuicebox function to export the list of DIRs as an annotations file for input into Juicebox. The Rao 2017 data are available in Juicebox by default under File > Open menu, “Rao et al. | Cell 2017”. We compared the data between the normal HCT-116 cells and the cells treated with auxin for 6 hours. For our example, we will use the data from Rao 2017.
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