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annotate shm_first.htm @ 0:64d74ba01a7c draft

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"planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
author rhpvorderman
date Wed, 27 Oct 2021 12:34:47 +0000
parents
children 495a521cf9f2
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1 <html>
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2
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3 <head>
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4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
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5 <meta name=Generator content="Microsoft Word 14 (filtered)">
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6 <style>
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7 <!--
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8 /* Font Definitions */
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9 @font-face
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10 {font-family:Calibri;
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11 panose-1:2 15 5 2 2 2 4 3 2 4;}
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12 /* Style Definitions */
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13 p.MsoNormal, li.MsoNormal, div.MsoNormal
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14 {margin-top:0in;
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15 margin-right:0in;
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16 margin-bottom:10.0pt;
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17 margin-left:0in;
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18 line-height:115%;
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19 font-size:11.0pt;
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20 font-family:"Calibri","sans-serif";}
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21 .MsoChpDefault
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22 {font-family:"Calibri","sans-serif";}
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23 .MsoPapDefault
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24 {margin-bottom:10.0pt;
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25 line-height:115%;}
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26 @page WordSection1
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27 {size:8.5in 11.0in;
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28 margin:1.0in 1.0in 1.0in 1.0in;}
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29 div.WordSection1
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30 {page:WordSection1;}
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31 -->
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32 </style>
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33
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34 </head>
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35
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36 <body lang=EN-US>
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37
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38 <div class=WordSection1>
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39
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40 <p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt;
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41 text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
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42 font-family:"Times New Roman","serif"'>Table showing the order of each
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43 filtering step and the number and percentage of sequences after each filtering
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44 step. </span></p>
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45
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46 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
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47 text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size:
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48 12.0pt;font-family:"Times New Roman","serif"'>Input:</span></u><span
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49 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The
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50 number of sequences in the original IMGT file. This is always 100% of the
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51 sequences.</span></p>
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52
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53 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
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54 text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size:
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55 12.0pt;font-family:"Times New Roman","serif"'>After &quot;no results&quot; filter: </span></u><span
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56 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IMGT
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57 classifies sequences either as &quot;productive&quot;, &quot;unproductive&quot;, &quot;unknown&quot;, or &quot;no
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58 results&quot;. Here, the number and percentages of sequences that are not classified
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59 as &quot;no results&quot; are reported.</span></p>
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60
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61 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
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62 text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size:
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63 12.0pt;font-family:"Times New Roman","serif"'>After functionality filter:</span></u><span
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64 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The
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65 number and percentages of sequences that have passed the functionality filter. The
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66 filtering performed is dependent on the settings of the functionality filter.
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67 Details on the functionality filter <a name="OLE_LINK12"></a><a
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68 name="OLE_LINK11"></a><a name="OLE_LINK10">can be found on the start page of
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69 the SHM&amp;CSR pipeline</a>.</span></p>
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70
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71 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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72 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
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73 removal sequences that are missing a gene region:</span></u><span lang=EN-GB
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74 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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75 In this step all sequences that are missing a gene region (FR1, CDR1, FR2,
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76 CDR2, FR3) that should be present are removed from analysis. The sequence
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77 regions that should be present are dependent on the settings of the sequence
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78 starts at filter. <a name="OLE_LINK9"></a><a name="OLE_LINK8">The number and
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79 percentage of sequences that pass this filter step are reported.</a> </span></p>
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80
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81 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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82 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
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83 N filter:</span></u><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
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84 font-family:"Times New Roman","serif"'> In this step all sequences that contain
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85 an ambiguous base (n) in the analysed region or the CDR3 are removed from the
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86 analysis. The analysed region is determined by the setting of the sequence
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87 starts at filter. The number and percentage of sequences that pass this filter
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88 step are reported.</span></p>
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89
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90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
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92 filter unique sequences</span></u><span lang=EN-GB style='font-size:12.0pt;
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93 line-height:115%;font-family:"Times New Roman","serif"'>: The number and
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94 percentage of sequences that pass the &quot;filter unique sequences&quot; filter. Details
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95 on this filter </span><span lang=EN-GB style='font-size:12.0pt;line-height:
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96 115%;font-family:"Times New Roman","serif"'>can be found on the start page of
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97 the SHM&amp;CSR pipeline</span></p>
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98
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99 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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100 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
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101 remove duplicate based on filter:</span></u><span lang=EN-GB style='font-size:
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102 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> The number and
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103 percentage of sequences that passed the remove duplicate filter. Details on the
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104 &quot;remove duplicate filter based on filter&quot; can be found on the start page of the
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105 SHM&amp;CSR pipeline.</span></p>
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106
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107 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK17"></a><a
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108 name="OLE_LINK16"><u><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
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109 font-family:"Times New Roman","serif"'>Number of matches sequences:</span></u></a><span
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110 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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111 The number and percentage of sequences that passed all the filters described
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112 above and have a (sub)class assigned.</span></p>
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113
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114 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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115 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Number
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116 of unmatched sequences</span></u><span lang=EN-GB style='font-size:12.0pt;
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117 line-height:115%;font-family:"Times New Roman","serif"'>: The number and percentage
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118 of sequences that passed all the filters described above and do not have
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119 subclass assigned.</span></p>
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120
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121 <p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
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122
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123 </div>
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124
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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125 </body>
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126
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127 </html>