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# Loupe V(D)J Browser: User Interface

With the CD8+ cytotoxic T cell dataset loaded, let's take a quick tour of the Loupe V(D)J Browser user interface.

## Summary Charts and Clonotype List

The Loupe V(D)J Browser interface consists of two main panels. On the left is the content panel. This is where most of the interaction and data display occurs. When you first load the dataset, the content panel displays a summary chart which shows the top 100 clonotypes, sorted by abundance. Above the chart are controls to change the type of chart, a few chart-specific options, and an export button.

### Clonotype List and Filter

On the right is the clonotype list, which initially displays the list of all clonotypes in the loaded sample. Each clonotype contains one or more (typically two) receptor chains, one per line. As indicated at the top of the clonotype list, the first column indicates the chain's type, here TRA or TRB. (If the sample included B cells, we would see types IGH, IGK, and IGL.) The next four columns, from left to right, display the V gene annotation, D gene annotation (if any), J gene annotation, and C gene annotation.

In the rightmost column is the clonotype barcode count which overlaps a bar to indicate that clonotype's relative frequency within the sample. You can hover over the bar to see the frequency of the clonotype as a percentage of total barcodes. The top clonotype in the tutorial sample should have 32 barcodes (1.6% of total).

Below the clonotype list are tools for filtering the clonotype list by gene, CDR3, and more. We'll explain how to use this in the next section, Filtering via the Clonotype List.

Between the clonotype list and the filter options is a gray bar indicating the current number of clonotypes in the list and the number of barcodes assigned to those clonotypes. These numbers are updated when clonotype filters are applied. To the right of this data is a download button, where you can export the current filtered or unfiltered clonotype list to a CSV as paired clonotypes or as single chains.

One of the major visualizations Loupe V(D)J Browser offers is the chain view, which shows how contigs assembled from each cell form a consensus V(D)J sequence of one chain of a clonotype. You can enable chain view by clicking on any chain in the clonotype list at right. Click the alpha chain on the top clonotype (TRAV13-1/TRAJ49/TRAC), and you should see something like this: