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annotate shm_clonality.htm @ 98:d714f5ea83d7 draft

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planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents 6809c63d9161
children
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1 <html>
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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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60 font-family:"Tahoma","sans-serif";}
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72 -->
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73 </style>
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74
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75 </head>
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76
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77 <body lang=EN-US link=blue vlink=purple>
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79 <div class=WordSection1>
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80
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81 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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82 text-align:justify;background:white'><b><span lang=EN-GB style='color:black'>References</span></b></p>
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83
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84 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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85 text-align:justify;background:white'><span lang=EN-GB style='color:black'>Gupta,
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86 Namita T. and Vander Heiden, Jason A. and Uduman, Mohamed and Gadala-Maria,
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87 Daniel and Yaari, Gur and Kleinstein, Steven H. (2015). <a name="OLE_LINK106"></a><a
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88 name="OLE_LINK107"></a>Change-O: a toolkit for analyzing large-scale B cell
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89 immunoglobulin repertoire sequencing data: Table 1. In<span
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90 class=apple-converted-space>&nbsp;</span><em>Bioinformatics, 31 (20), pp.
90
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91 3356–3358.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><a
83
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92 href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
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93 lang=EN-GB style='color:#303030'>doi:10.1093/bioinformatics/btv359</span></a><span
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94 lang=EN-GB style='color:black'>][</span><a
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95 href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
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96 lang=EN-GB style='color:#303030'>Link</span></a><span lang=EN-GB
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97 style='color:black'>]</span></p>
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98
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99 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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100 text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
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101
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102 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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103 text-align:justify;background:white'><a name="OLE_LINK110"><u><span lang=EN-GB
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104 style='color:black'>All, IGA, IGG, IGM and IGE tabs</span></u></a></p>
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105
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106 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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107 text-align:justify;background:white'><span lang=EN-GB style='color:black'>In
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108 these tabs information on the clonal relation of transcripts can be found. To
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109 calculate clonal relation Change-O is used (Gupta et al, PMID: 26069265).
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110 Transcripts are considered clonally related if they have maximal three nucleotides
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111 difference in their CDR3 sequence and the same first V segment (as assigned by
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112 IMGT). Results are represented in a table format showing the clone size and the
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113 number of clones or sequences with this clone size. Change-O settings used are
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114 the </span><span lang=EN-GB>nucleotide hamming distance substitution model with
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115 a complete distance of maximal three. For clonal assignment the first gene
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116 segments were used, and the distances were not normalized. In case of
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117 asymmetric distances, the minimal distance was used.<span style='color:black'> </span></span></p>
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118
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119 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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120 text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
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121
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122 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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123 text-align:justify;background:white'><u><span lang=EN-GB style='color:black'>Overlap
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124 tab</span></u><span lang=EN-GB style='color:black'> </span></p>
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125
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126 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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127 text-align:justify;background:white'><span lang=EN-GB style='color:black'>This
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128 tab gives information on with which (sub)classe(s) each unique analyzed region
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129 (based on the exact nucleotide sequence of the analyzes region and the CDR3
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130 nucleotide sequence) is found with. This gives information if the combination
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131 of the exact same nucleotide sequence of the analyzed region and the CDR3
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132 sequence can be found in multiple (sub)classes.</span></p>
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133
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134 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
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135 text-align:justify;background:white'><span style='color:black'><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC"> Please note that this tab is based on all
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136 sequences before filter unique sequences and the remove duplicates based on
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137 filters are applied. In this table only sequences occuring more than once are
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138 included. </span></p>
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139
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140 </div>
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141
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142 </body>
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143
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144 </html>