Mercurial > repos > davidvanzessen > argalaxy_tools

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"planemo upload commit 1a7731bb4fe2e80fb1fdc88121783068af3edb08"
author rhpvorderman
date Fri, 21 Apr 2023 10:04:39 +0000
parents 81b3eb11ed2c
children
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1 <html>
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3 <head>
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4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8">
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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='text-align:justify'><b><u><span
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41 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
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42 tab</span></u></b></p>
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43
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44 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
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45 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Description</span></b></p>
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46
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47 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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48 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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49 filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%;
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50 font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a
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51 name="OLE_LINK14">Allows you to download information on V D and J gene usage,
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52 the junctions and the amino acid sequence of the sequences that passed the chosen
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53 filter settings. Note: this file contains only 1 sequences of a replicate
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54 sequence. </a></span></p>
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55
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56 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
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57 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene
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58 frequencies</span></b></p>
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59
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60 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
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61 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
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62 font-family:"Times New Roman","serif"'>The dataset used to generate the distribution
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63 of V gene families graph:</span></u><span style='font-size:12.0pt;font-family:
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64 "Times New Roman","serif"'> Downloads a table with information used to generate
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65 the distribution of V gene families graph.</span></p>
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66
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67 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
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68 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
58
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69 font-family:"Times New Roman","serif"'>The dataset used to generate  the
54
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70 distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
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71 font-family:"Times New Roman","serif"'>Downloads a table with information used
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72 to generate the distribution of D gene families graph.</span></p>
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73
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74 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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75 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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76 dataset used to generate the relative frequency of V gene usage graph:</span></u><span
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77 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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78 Downloads the data used to generate the relative frequency of V gene usage
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79 graph. In addition information on the chromosomal order of the V genes can be
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80 found.</span></p>
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81
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82 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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83 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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84 dataset used to generate the relative frequency of D gene usage graph:</span></u><span
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85 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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86 Downloads the data used to generate the relative frequency of D gene usage
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87 graph. In addition information on the chromosomal order of the D genes can be
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88 found.<u> </u></span></p>
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89
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90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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92 dataset used to generate the relative frequency of J gene usage graph: </span></u><span
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93 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
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94 the data used to generate the relative frequency of J gene usage graph. In
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95 addition information on the chromosomal order of the J genes can be found.<u> </u></span></p>
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96
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97 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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98 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
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99 color:black'>The dataset used to generate the relative frequency of the D
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100 reading frame graph</span></u><span lang=EN-GB style='font-size:12.0pt;
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101 line-height:115%;font-family:"Times New Roman","serif";color:black'>: Downloads
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102 the data used to generate the relative frequency of the D reading frame. </span></p>
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103
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104 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
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105 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
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106 color:black'>CDR3 characteristics</span></b></p>
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107
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108 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
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109 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
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110 font-family:"Times New Roman","serif"'>The dataset used to generate the CDR3
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111 length frequency graph:</span></u><span style='font-size:12.0pt;font-family:
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112 "Times New Roman","serif"'> Downloads a table with information used for the
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113 length distribution of CDR3 plot. </span></p>
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114
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115 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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116 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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117 dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span
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118 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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119 Downloads the frequency of the different amino acids in the CDR3 of all
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120 filtered sequences. This data set is used for the generation of the Amino Acid
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121 Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
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122 in included. </span></p>
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123
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124 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
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125 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Heatmaps</span></b></p>
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126
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127 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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128 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
58
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129 data used to generate the VD heatmap for “donor name”:</span></u><span
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130 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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131 Downloads the data set used for the generation of the VD heatmap. For each
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132 uploaded donor a separate download is generated.</span></p>
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133
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134 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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135 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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136 data used to generate the VJ heatmap for “donor name”:</span></u><span
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137 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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138 Downloads the data set used for the generation of the VJ heatmap. For each
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139 uploaded donor a separate download is generated.</span></p>
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140
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141 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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142 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
58
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143 data used to generate the DJ heatmap for “sample name”:</span></u><span
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144 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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145 Downloads the data set used for the generation of the DJ heatmap. For each
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146 uploaded donor a separate download is generated.</span></p>
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147
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148 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
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149 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Circos</span></b></p>
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150
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151 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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152 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
58
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153 data used to generate the VD circus plots for “donor name”:</span></u><span
54
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154 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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155 Downloads the data set used for the generation of the VD heatmap. For each
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156 uploaded donor a separate download is generated.</span></p>
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157
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158 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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159 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
58
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160 data used to generate the VJ circus plots for “donor name”:</span></u><span
54
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161 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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162 Downloads the data set used for the generation of the VJ heatmap. For each
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163 uploaded donor a separate download is generated.</span></p>
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164
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165 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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166 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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167 data used to generate the DJ circus plots for “sample name”:</span></u><span
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168 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
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169 Downloads the data set used for the generation of the DJ heatmap. For each
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170 uploaded donor a separate download is generated.</span></p>
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171
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172 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
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173 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p>
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174
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175 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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176 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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177 dataset used to calculate clonality score: </span></u><span style='font-size:
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178 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
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179 download information on V D and J gene usage, the junctions and the amino acid
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180 sequence of the sequences that passed the chosen filter settings. Note: this
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181 file contains all the replicate sequences form the different input files.</span></p>
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182
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183 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
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184 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences
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185 that are present in more than one replicate:</span></u><span style='font-size:
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186 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to
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187 download a table containing all the sequences that were present in more than
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188 one replicate. It provides the concidence type, clonaltype, sequence name,
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189 replicate number, and the nucleotide sequence</span></p>
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190
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191 <p class=MsoNormal>&nbsp;</p>
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192
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193 </div>
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194
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195 </body>
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196
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197 </html>