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comparison report_clonality/naive_downloads.htm @ 27:b539aeb75980 draft

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author davidvanzessen
date Tue, 28 Feb 2017 08:10:34 -0500
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41 <body lang=EN-US> 36 <body lang=EN-US>
42 37
43 <div class=WordSection1> 38 <div class=WordSection1>
44 39
45 <p class=MsoNormalCxSpFirst style='text-align:justify'><u><span 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
46 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The 48 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%; 49 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 50 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, 51 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 52 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 53 filter settings. Note: this file contains only 1 sequences of a replicate
52 sequence. </a></span></p> 54 sequence. </a></span></p>
53 55
54 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 56 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
55 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The 57 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene
56 dataset used to calculate clonality score: </span></u><span style='font-size: 58 frequencies</span></b></p>
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 59
69 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; 60 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
70 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; 61 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 62 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: 63 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 64 "Times New Roman","serif"'> Downloads a table with information used to generate
74 the distribution of V gene families graph. </span></p> 65 the distribution of V gene families graph.</span></p>
75 66
76 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; 67 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
77 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; 68 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 69 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; 70 distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
84 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The 75 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 76 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"'> 77 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 78 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 79 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; 80 found.</span></p>
90 line-height:115%;font-family:"Times New Roman","serif"'> </span></u></p>
91 81
92 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 82 <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 83 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 84 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"'> 85 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 86 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 87 graph. In addition information on the chromosomal order of the D genes can be
98 found. </span></p> 88 found.<u> </u></span></p>
99 89
100 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 90 <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 91 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 92 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 93 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 94 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> 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>
106 114
107 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 115 <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 116 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 117 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"'> 118 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 119 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 120 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 121 Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
114 in included. </span></p> 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>
115 126
116 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 127 <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 128 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 129 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"'> 130 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 138 Downloads the data set used for the generation of the VJ heatmap. For each
128 uploaded donor a separate download is generated.</span></p> 139 uploaded donor a separate download is generated.</span></p>
129 140
130 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 141 <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 142 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
132 data used to generate the DJ heatmap for “donor name”:</span></u><span 143 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"'> 144 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 145 Downloads the data set used for the generation of the DJ heatmap. For each
135 uploaded donor a separate download is generated.</span></p> 146 uploaded donor a separate download is generated.</span></p>
136 147
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
137 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span 151 <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 152 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
139 frequency count of a clonotype:</span></u><span style='font-size:12.0pt; 153 data used to generate the VD circus plots for “donor name”:</span></u><span
140 line-height:115%;font-family:"Times New Roman","serif"'> The frequency count of 154 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
141 a clonotype in the unfiltered data set. The clonotype defition used is defined 155 Downloads the data set used for the generation of the VD heatmap. For each
142 in the ‘clonal type definition’ filter. </span></p> 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>
143 190
144 <p class=MsoNormal>&nbsp;</p> 191 <p class=MsoNormal>&nbsp;</p>
145 192
146 </div> 193 </div>
147 194