Mercurial > repos > davidvanzessen > argalaxy_tools

annotate report_clonality/naive_junction.htm @ 54:81b3eb11ed2c draft

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"planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
author rhpvorderman
date Tue, 16 Nov 2021 15:42:32 +0000
parents 124b7fd92a3e
children 4c6df851e262
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1 <html xmlns:v="urn:schemas-microsoft-com:vml"
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2 xmlns:o="urn:schemas-microsoft-com:office:office"
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3 xmlns:w="urn:schemas-microsoft-com:office:word"
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4 xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
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5 xmlns="http://www.w3.org/TR/REC-html40">
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6
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7 <head>
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8 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
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9 <meta name=ProgId content=Word.Document>
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10 <meta name=Generator content="Microsoft Word 14">
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11 <meta name=Originator content="Microsoft Word 14">
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12 <link rel=File-List href="Junction%20analysis%20tab_files/filelist.xml">
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13 <link rel=themeData href="Junction%20analysis%20tab_files/themedata.thmx">
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14 <style>
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15 <!--
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16 /* Font Definitions */
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17 @font-face
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18 {font-family:Calibri;
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19 panose-1:2 15 5 2 2 2 4 3 2 4;
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20 mso-font-charset:0;
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21 mso-generic-font-family:swiss;
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22 mso-font-pitch:variable;
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23 mso-font-signature:-536870145 1073786111 1 0 415 0;}
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24 /* Style Definitions */
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25 p.MsoNormal, li.MsoNormal, div.MsoNormal
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26 {mso-style-unhide:no;
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27 mso-style-qformat:yes;
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28 mso-style-parent:"";
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29 margin-top:0in;
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30 margin-right:0in;
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31 margin-bottom:10.0pt;
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32 margin-left:0in;
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33 line-height:115%;
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34 mso-pagination:widow-orphan;
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35 font-size:11.0pt;
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36 font-family:"Calibri","sans-serif";
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37 mso-fareast-font-family:"Times New Roman";
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38 mso-fareast-theme-font:minor-fareast;
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39 mso-bidi-font-family:"Times New Roman";}
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40 p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
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41 {mso-style-priority:1;
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42 mso-style-unhide:no;
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43 mso-style-qformat:yes;
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44 margin:0in;
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45 margin-bottom:.0001pt;
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46 mso-pagination:widow-orphan;
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47 font-size:11.0pt;
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48 font-family:"Calibri","sans-serif";
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49 mso-fareast-font-family:"Times New Roman";
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50 mso-fareast-theme-font:minor-fareast;
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51 mso-bidi-font-family:"Times New Roman";}
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52 p.msochpdefault, li.msochpdefault, div.msochpdefault
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53 {mso-style-name:msochpdefault;
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54 mso-style-unhide:no;
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55 mso-margin-top-alt:auto;
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56 margin-right:0in;
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57 mso-margin-bottom-alt:auto;
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58 margin-left:0in;
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59 mso-pagination:widow-orphan;
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60 font-size:12.0pt;
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61 font-family:"Calibri","sans-serif";
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62 mso-fareast-font-family:"Times New Roman";
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63 mso-fareast-theme-font:minor-fareast;
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64 mso-bidi-font-family:"Times New Roman";}
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65 p.msopapdefault, li.msopapdefault, div.msopapdefault
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66 {mso-style-name:msopapdefault;
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67 mso-style-unhide:no;
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68 mso-margin-top-alt:auto;
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69 margin-right:0in;
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70 margin-bottom:10.0pt;
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71 margin-left:0in;
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72 line-height:115%;
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73 mso-pagination:widow-orphan;
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74 font-size:12.0pt;
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75 font-family:"Times New Roman","serif";
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76 mso-fareast-font-family:"Times New Roman";
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77 mso-fareast-theme-font:minor-fareast;}
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78 span.GramE
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79 {mso-style-name:"";
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80 mso-gram-e:yes;}
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81 .MsoChpDefault
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82 {mso-style-type:export-only;
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83 mso-default-props:yes;
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84 font-size:10.0pt;
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85 mso-ansi-font-size:10.0pt;
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86 mso-bidi-font-size:10.0pt;
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87 font-family:"Calibri","sans-serif";
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88 mso-ascii-font-family:Calibri;
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89 mso-hansi-font-family:Calibri;}
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90 .MsoPapDefault
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91 {mso-style-type:export-only;
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92 margin-bottom:10.0pt;
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93 line-height:115%;}
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94 @page WordSection1
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95 {size:8.5in 11.0in;
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96 margin:1.0in 1.0in 1.0in 1.0in;
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97 mso-header-margin:.5in;
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98 mso-footer-margin:.5in;
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99 mso-paper-source:0;}
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100 div.WordSection1
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101 {page:WordSection1;}
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102 -->
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103 </style>
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104 <!--[if gte mso 10]>
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105 <style>
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106 /* Style Definitions */
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107 table.MsoNormalTable
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108 {mso-style-name:"Table Normal";
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109 mso-tstyle-rowband-size:0;
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110 mso-tstyle-colband-size:0;
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111 mso-style-noshow:yes;
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112 mso-style-priority:99;
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113 mso-style-parent:"";
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114 mso-padding-alt:0in 5.4pt 0in 5.4pt;
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115 mso-para-margin-top:0in;
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116 mso-para-margin-right:0in;
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117 mso-para-margin-bottom:10.0pt;
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118 mso-para-margin-left:0in;
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119 line-height:115%;
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120 mso-pagination:widow-orphan;
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121 font-size:10.0pt;
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122 font-family:"Calibri","sans-serif";}
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123 </style>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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124 <![endif]--><!--[if gte mso 9]><xml>
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125 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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126 </xml><![endif]--><!--[if gte mso 9]><xml>
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127 <o:shapelayout v:ext="edit">
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128 <o:idmap v:ext="edit" data="1"/>
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129 </o:shapelayout></xml><![endif]-->
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130 </head>
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131
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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132 <body lang=EN-US style='tab-interval:.5in'>
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133
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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134 <div class=WordSection1>
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135
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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136 <p class=MsoNormal style='text-align:justify'><b><u><span style='font-size:
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137 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Junction
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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138 analysis tab </span></u></b></p>
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139
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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140 <p class=MsoNormal style='text-align:justify'><b><span style='font-size:12.0pt;
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141 line-height:115%;font-family:"Times New Roman","serif"'>Tables:</span></b></p>
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142
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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143 <p class=MsoNormal style='text-align:justify'><span style='font-size:12.0pt;
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144 line-height:115%;font-family:"Times New Roman","serif"'>The unique
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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145 rearrangements are separated in sequences that contain <span class=GramE>both a</span>
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146 V, D and J gene and sequences that contain only a V and J gene.</span></p>
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147
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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148 <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
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149 justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
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150 font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Productive mean
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151 tables<o:p></o:p></span></u></p>
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152
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153 <p class=MsoNormal style='text-align:justify'><span class=GramE><span
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154 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports
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155 for each donor the number of productive sequences and the mean number of
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156 deletions, N-nucleotides and P-nucleotides.</span></span><span
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157 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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158 For explanation about the different deletions and N and P nucleotides see
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159 figure above. </span></p>
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160
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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161 <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
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162 justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
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163 font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Unproductive
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164 mean table<o:p></o:p></span></u></p>
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165
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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166 <p class=MsoNormal style='text-align:justify'><span class=GramE><span
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167 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports
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168 for each donor the number of unproductive sequences and the mean number of
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169 deletions, N-nucleotides and P-nucleotides.</span></span><span
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170 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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171 For explanation about the different deletions and N and P nucleotides see
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172 figure above. </span></p>
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173
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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174 <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
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175 justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
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176 font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Productive
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177 median table<o:p></o:p></span></u></p>
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178
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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179 <p class=MsoNormal style='text-align:justify'><span class=GramE><span
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180 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports
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181 for each donor the number of productive sequences and the median number of
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182 deletions, N-nucleotides and P-nucleotides.</span></span><span
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183 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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184 For explanation about the different deletions and N and P nucleotides see
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185 figure above. </span></p>
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186
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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187 <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
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188 justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
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189 font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Unproductive
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190 median table<o:p></o:p></span></u></p>
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191
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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192 <p class=MsoNormal style='text-align:justify'><span class=GramE><span
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193 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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194 for each donor the number of unproductive sequences and the median number of
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195 deletions, N-nucleotides and P-nucleotides.</span></span><span
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196 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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197 For explanation about the different deletions and N and P nucleotides see
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198 figure above. </span></p>
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199
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200 <p class=MsoNormal>&nbsp;</p>
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201
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202 </div>
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203
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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204 </body>
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205
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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206 </html>