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comparison report_clonality/naive_downloads.htm @ 18:5d11c9139a55 draft

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author davidvanzessen
date Wed, 21 Dec 2016 11:53:03 -0500
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17:da95be204ebc 18:5d11c9139a55
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3 <head>
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
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41 <body lang=EN-US>
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43 <div class=WordSection1>
44
45 <p class=MsoNormalCxSpFirst style='text-align:justify'><u><span
46 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
47 filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%;
48 font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a
49 name="OLE_LINK14">Allows you to download information on V D and J gene usage,
50 the junctions and the amino acid sequence of the sequences that passed the chosen
51 filter settings. Note: this file contains only 1 sequences of a replicate
52 sequence. </a></span></p>
53
54 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
55 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
56 dataset used to calculate clonality score: </span></u><span style='font-size:
57 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
58 download information on V D and J gene usage, the junctions and the amino acid
59 sequence of the sequences that passed the chosen filter settings. Note: this
60 file contains all the replicate sequences form the different input files.</span></p>
61
62 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
63 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
64 font-family:"Times New Roman","serif"'>The dataset used to generate the CDR3
65 length frequency graph:</span></u><span style='font-size:12.0pt;font-family:
66 "Times New Roman","serif"'> Downloads a table with information used for the
67 length distribution of CDR3 plot. </span></p>
68
69 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
70 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
71 font-family:"Times New Roman","serif"'>The dataset used to generate the distribution
72 of V gene families graph:</span></u><span style='font-size:12.0pt;font-family:
73 "Times New Roman","serif"'> Downloads a table with information used to generate
74 the distribution of V gene families graph. </span></p>
75
76 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
77 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
78 font-family:"Times New Roman","serif"'>The dataset used to generate  the
79 distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
80 font-family:"Times New Roman","serif"'>Downloads a table with information used
81 to generate the distribution of D gene families graph.</span></p>
82
83 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
84 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
85 dataset used to generate the relative frequency of V gene usage graph:</span></u><span
86 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
87 Downloads the data used to generate the relative frequency of V gene usage
88 graph. In addition information on the chromosomal order of the V genes can be
89 found</span><span lang=EN-GB>.</span><u><span lang=EN-GB style='font-size:12.0pt;
90 line-height:115%;font-family:"Times New Roman","serif"'> </span></u></p>
91
92 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
93 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
94 dataset used to generate the relative frequency of D gene usage graph:</span></u><span
95 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
96 Downloads the data used to generate the relative frequency of D gene usage
97 graph. In addition information on the chromosomal order of the D genes can be
98 found. </span></p>
99
100 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
101 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
102 dataset used to generate the relative frequency of J gene usage graph: </span></u><span
103 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
104 the data used to generate the relative frequency of J gene usage graph. In
105 addition information on the chromosomal order of the J genes can be found.</span></p>
106
107 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
108 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
109 dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span
110 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
111 Downloads the frequency of the different amino acids in the CDR3 of all
112 filtered sequences. This data set is used for the generation of the Amino Acid
113 Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
114 in included. </span></p>
115
116 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
117 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
118 data used to generate the VD heatmap for “donor name”:</span></u><span
119 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
120 Downloads the data set used for the generation of the VD heatmap. For each
121 uploaded donor a separate download is generated.</span></p>
122
123 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
124 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
125 data used to generate the VJ heatmap for “donor name”:</span></u><span
126 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
127 Downloads the data set used for the generation of the VJ heatmap. For each
128 uploaded donor a separate download is generated.</span></p>
129
130 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
131 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
132 data used to generate the DJ heatmap for “sample name”:</span></u><span
133 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
134 Downloads the data set used for the generation of the DJ heatmap. For each
135 uploaded donor a separate download is generated.</span></p>
136
137 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
138 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>A
139 frequency count of a clonotype:</span></u><span style='font-size:12.0pt;
140 line-height:115%;font-family:"Times New Roman","serif"'> The frequency count of
141 a clonotype in the unfiltered data set. The clonotype defition used is defined
142 in the ‘clonal type definition’ filter. </span></p>
143
144 <p class=MsoNormal>&nbsp;</p>
145
146 </div>
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148 </body>
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150 </html>