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1 <!DOCTYPE html>
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2 <html lang="en">
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3 <head>
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4 <meta charset="utf-8">
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5 <!--<link rel="stylesheet" href="style/base.css" type="text/css" />-->
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6 </head>
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7 <body style="margin-left: 1cm">
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8 <div class="jumbotron">
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9 <div class="container">
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10 <h3>Test Data Name Conventions</h3>
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11 <p>Concerning the naming of the execution parameters, input and output files, the following convention applies: </p>
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12 <ul>
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13 <li class="container">The name starts with the tool specifier; see Tool Specifiers Table below.</li>
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14 <li class="container">The clonotype definition specifier follows, if needed; see Clonotype Definition Specifiers Table below.</li>
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15 <li class="container">The gene specifier (geneV or geneJ) follows, if needed.</li>
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16 <li class="container">The cell type specifier (BCR or TCR) follows.</li>
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17 <li class="container">The name ends with the file content specifier (input, output or parameters).</li>
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18 </ul>
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19
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20 <p><i>Tool Specifiers Table</i></p>
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21 <table style="border-spacing: 10px 0px">
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22 <tr align="left">
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23 <th>Index</th>
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24 <th>Tool</th>
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25 <th>Specifier</th>
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26 </tr>
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27 <tr>
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28 <td>1</td>
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29 <td>Data Filtering</td>
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30 <td>data_filter</td>
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31 </tr>
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32 <tr>
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33 <td>2</td>
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34 <td>Clonotype Diversity & Expression</td>
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35 <td>clono_compute</td>
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36 </tr>
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37 <tr>
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38 <td>3</td>
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39 <td>Gene Usage</td>
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40 <td>gene_usage</td>
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41 </tr>
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42 <tr>
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43 <td>4</td>
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44 <td>Public Clonotypes</td>
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45 <td>public_clonos</td>
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46 </tr>
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47 <tr>
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48 <td>5</td>
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49 <td>Exclusive Clonotypes</td>
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50 <td>exclusive_clonos</td>
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51 </tr>
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52 <tr>
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53 <td>6</td>
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54 <td>Gene Usage Comparison</td>
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55 <td>gene_compare</td>
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56 </tr>
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57 </table>
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58
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59 <br>
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60
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61 <p><i>Clonotype Definition Specifiers Table</i></p>
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62 <table style="border-spacing: 10px 0px">
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63 <tr align="left">
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64 <th>Index</th>
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65 <th>Clonotype Definition</th>
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66 <th>Specifier</th>
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67 </tr>
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68 <tr>
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69 <td>1</td>
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70 <td>CDR3</td>
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71 <td>def1</td>
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72 </tr>
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73 <tr>
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74 <td>2</td>
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75 <td>V+CDR3</td>
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76 <td>def2</td>
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77 </tr>
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78 <tr>
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79 <td>3</td>
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80 <td>J+CDR3</td>
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81 <td>def3</td>
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82 </tr>
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83 <tr>
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84 <td>4</td>
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85 <td>V+J+CDR3</td>
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86 <td>def4</td>
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87 </tr>
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88 <tr>
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89 <td>5</td>
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90 <td>V+D+J+CDR3</td>
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91 <td>def5</td>
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92 </tr>
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93 </table>
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