46
|
1 <html>
|
|
2
|
|
3 <head>
|
|
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
|
|
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
|
|
6 <style>
|
|
7 <!--
|
|
8 /* Font Definitions */
|
|
9 @font-face
|
|
10 {font-family:Calibri;
|
|
11 panose-1:2 15 5 2 2 2 4 3 2 4;}
|
|
12 /* Style Definitions */
|
|
13 p.MsoNormal, li.MsoNormal, div.MsoNormal
|
|
14 {margin-top:0in;
|
|
15 margin-right:0in;
|
|
16 margin-bottom:10.0pt;
|
|
17 margin-left:0in;
|
|
18 line-height:115%;
|
|
19 font-size:11.0pt;
|
|
20 font-family:"Calibri","sans-serif";}
|
|
21 .MsoChpDefault
|
|
22 {font-family:"Calibri","sans-serif";}
|
|
23 .MsoPapDefault
|
|
24 {margin-bottom:10.0pt;
|
|
25 line-height:115%;}
|
|
26 @page WordSection1
|
|
27 {size:8.5in 11.0in;
|
|
28 margin:1.0in 1.0in 1.0in 1.0in;}
|
|
29 div.WordSection1
|
|
30 {page:WordSection1;}
|
|
31 -->
|
|
32 </style>
|
|
33
|
|
34 </head>
|
|
35
|
|
36 <body lang=EN-US>
|
|
37
|
|
38 <div class=WordSection1>
|
|
39
|
|
40 <p class=MsoNormalCxSpFirst style='text-align:justify'><b><u><span
|
|
41 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
|
|
42 tab</span></u></b></p>
|
|
43
|
|
44 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
|
|
45 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Description</span></b></p>
|
|
46
|
|
47 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
48 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
49 filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%;
|
|
50 font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a
|
|
51 name="OLE_LINK14">Allows you to download information on V D and J gene usage,
|
|
52 the junctions and the amino acid sequence of the sequences that passed the chosen
|
|
53 filter settings. Note: this file contains only 1 sequences of a replicate
|
|
54 sequence. </a></span></p>
|
|
55
|
|
56 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
|
|
57 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene
|
|
58 frequencies</span></b></p>
|
|
59
|
|
60 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
|
|
61 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
|
|
62 font-family:"Times New Roman","serif"'>The dataset used to generate the distribution
|
|
63 of V gene families graph:</span></u><span style='font-size:12.0pt;font-family:
|
|
64 "Times New Roman","serif"'> Downloads a table with information used to generate
|
|
65 the distribution of V gene families graph.</span></p>
|
|
66
|
|
67 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
|
|
68 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
|
|
69 font-family:"Times New Roman","serif"'>The dataset used to generate the
|
|
70 distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
|
|
71 font-family:"Times New Roman","serif"'>Downloads a table with information used
|
|
72 to generate the distribution of D gene families graph.</span></p>
|
|
73
|
|
74 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
75 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
76 dataset used to generate the relative frequency of V gene usage graph:</span></u><span
|
|
77 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
78 Downloads the data used to generate the relative frequency of V gene usage
|
|
79 graph. In addition information on the chromosomal order of the V genes can be
|
|
80 found.</span></p>
|
|
81
|
|
82 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
83 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
84 dataset used to generate the relative frequency of D gene usage graph:</span></u><span
|
|
85 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
86 Downloads the data used to generate the relative frequency of D gene usage
|
|
87 graph. In addition information on the chromosomal order of the D genes can be
|
|
88 found.<u> </u></span></p>
|
|
89
|
|
90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
92 dataset used to generate the relative frequency of J gene usage graph: </span></u><span
|
|
93 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
|
|
94 the data used to generate the relative frequency of J gene usage graph. In
|
|
95 addition information on the chromosomal order of the J genes can be found.<u> </u></span></p>
|
|
96
|
|
97 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
|
|
98 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
|
|
99 color:black'>The dataset used to generate the relative frequency of the D
|
|
100 reading frame graph</span></u><span lang=EN-GB style='font-size:12.0pt;
|
|
101 line-height:115%;font-family:"Times New Roman","serif";color:black'>: Downloads
|
|
102 the data used to generate the relative frequency of the D reading frame. </span></p>
|
|
103
|
|
104 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
|
|
105 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
|
|
106 color:black'>CDR3 characteristics</span></b></p>
|
|
107
|
|
108 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
|
|
109 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
|
|
110 font-family:"Times New Roman","serif"'>The dataset used to generate the CDR3
|
|
111 length frequency graph:</span></u><span style='font-size:12.0pt;font-family:
|
|
112 "Times New Roman","serif"'> Downloads a table with information used for the
|
|
113 length distribution of CDR3 plot. </span></p>
|
|
114
|
|
115 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
116 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
117 dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span
|
|
118 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
119 Downloads the frequency of the different amino acids in the CDR3 of all
|
|
120 filtered sequences. This data set is used for the generation of the Amino Acid
|
|
121 Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
|
|
122 in included. </span></p>
|
|
123
|
|
124 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
|
|
125 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Heatmaps</span></b></p>
|
|
126
|
|
127 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
128 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
129 data used to generate the VD heatmap for “donor name”:</span></u><span
|
|
130 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
131 Downloads the data set used for the generation of the VD heatmap. For each
|
|
132 uploaded donor a separate download is generated.</span></p>
|
|
133
|
|
134 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
135 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
136 data used to generate the VJ heatmap for “donor name”:</span></u><span
|
|
137 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
138 Downloads the data set used for the generation of the VJ heatmap. For each
|
|
139 uploaded donor a separate download is generated.</span></p>
|
|
140
|
|
141 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
142 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
143 data used to generate the DJ heatmap for “sample name”:</span></u><span
|
|
144 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
145 Downloads the data set used for the generation of the DJ heatmap. For each
|
|
146 uploaded donor a separate download is generated.</span></p>
|
|
147
|
|
148 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
|
|
149 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Circos</span></b></p>
|
|
150
|
|
151 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
152 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
153 data used to generate the VD circus plots for “donor name”:</span></u><span
|
|
154 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
155 Downloads the data set used for the generation of the VD heatmap. For each
|
|
156 uploaded donor a separate download is generated.</span></p>
|
|
157
|
|
158 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
159 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
160 data used to generate the VJ circus plots for “donor name”:</span></u><span
|
|
161 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
162 Downloads the data set used for the generation of the VJ heatmap. For each
|
|
163 uploaded donor a separate download is generated.</span></p>
|
|
164
|
|
165 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
166 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
167 data used to generate the DJ circus plots for “sample name”:</span></u><span
|
|
168 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
|
|
169 Downloads the data set used for the generation of the DJ heatmap. For each
|
|
170 uploaded donor a separate download is generated.</span></p>
|
|
171
|
|
172 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
|
|
173 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p>
|
|
174
|
|
175 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
176 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
|
|
177 dataset used to calculate clonality score: </span></u><span style='font-size:
|
|
178 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
|
|
179 download information on V D and J gene usage, the junctions and the amino acid
|
|
180 sequence of the sequences that passed the chosen filter settings. Note: this
|
|
181 file contains all the replicate sequences form the different input files.</span></p>
|
|
182
|
|
183 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
|
|
184 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences
|
|
185 that are present in more than one replicate:</span></u><span style='font-size:
|
|
186 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to
|
|
187 download a table containing all the sequences that were present in more than
|
|
188 one replicate. It provides the concidence type, clonaltype, sequence name,
|
|
189 replicate number, and the nucleotide sequence</span></p>
|
|
190
|
|
191 <p class=MsoNormal> </p>
|
|
192
|
|
193 </div>
|
|
194
|
|
195 </body>
|
|
196
|
|
197 </html>
|