annotate shm_csr.htm @ 98:d714f5ea83d7 draft default tip

planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents 6809c63d9161
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
67
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
1 <html>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
2
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
3 <head>
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 67
diff changeset
4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8">
67
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
6 <style>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
7 <!--
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
8 /* Font Definitions */
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
9 @font-face
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
10 {font-family:Calibri;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
11 panose-1:2 15 5 2 2 2 4 3 2 4;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
12 /* Style Definitions */
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
13 p.MsoNormal, li.MsoNormal, div.MsoNormal
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
14 {margin-top:0in;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
15 margin-right:0in;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
16 margin-bottom:10.0pt;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
17 margin-left:0in;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
18 line-height:115%;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
19 font-size:11.0pt;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
20 font-family:"Calibri","sans-serif";}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
21 a:link, span.MsoHyperlink
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
22 {color:blue;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
23 text-decoration:underline;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
24 a:visited, span.MsoHyperlinkFollowed
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
25 {color:purple;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
26 text-decoration:underline;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
27 span.apple-converted-space
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
28 {mso-style-name:apple-converted-space;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
29 .MsoChpDefault
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
30 {font-family:"Calibri","sans-serif";}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
31 .MsoPapDefault
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
32 {margin-bottom:10.0pt;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
33 line-height:115%;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
34 @page WordSection1
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
35 {size:8.5in 11.0in;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
36 margin:1.0in 1.0in 1.0in 1.0in;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
37 div.WordSection1
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
38 {page:WordSection1;}
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
39 -->
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
40 </style>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
41
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
42 </head>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
43
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
44 <body lang=EN-US link=blue vlink=purple>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
45
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
46 <div class=WordSection1>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
47
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
48 <p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
49 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
50 graphs in this tab give insight into the subclass distribution of IGG and IGA
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
51 transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 67
diff changeset
52 font-family:"Times New Roman","serif"'>Human Cµ, C&#945;, C&#947; and C&#949;
67
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
53 constant genes are assigned using a </span><span lang=EN-GB style='font-size:
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
54 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
55 specifically designed for human (sub)class assignment in repertoire data as
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
56 described in van Schouwenburg and IJspeert et al, submitted for publication. In
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
57 this script the reference sequences for the subclasses are divided in 8
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
58 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
59 then individually aligned in the right order to each input sequence. The
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
60 percentage of the chunks identified in each rearrangement is calculated in the
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 67
diff changeset
61 ‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt;
67
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
62 line-height:115%;font-family:"Times New Roman","serif"'>C&#945; and C&#947;
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
63 subclasses are very homologous and only differ in a few nucleotides. To assign
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
64 subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height:
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 67
diff changeset
65 115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated.
67
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
66 This percentage indicates how well the chunks covering the subclass specific
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
67 nucleotide match with the different subclasses. </span><span lang=EN-GB
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
68 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
69 on normal distribution of subclasses in healthy individuals of different ages
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
70 can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
71
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
73 name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
74 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
75 subclass distribution</span></u></a></p>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
76
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
77 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
78 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
79 chart showing the relative distribution of IGA1 and IGA2 transcripts in the
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
80 sample.</span></p>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
81
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
82 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
83 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
84 subclass distribution</span></u></p>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
85
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
86 <p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
88 chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
89 transcripts in the sample.</span></p>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
90
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
91 </div>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
92
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
93 </body>
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
94
ba33b94637ca Uploaded
davidvanzessen
parents: 39
diff changeset
95 </html>