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"planemo upload commit 05326cc2233eb0fa8beaf4198bd7c1519f2a0bf9"
author rhpvorderman
date Mon, 15 Nov 2021 14:04:10 +0000
parents 64d74ba01a7c
children 495a521cf9f2
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1 <html>
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2
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3 <head>
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4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
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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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11 panose-1:2 15 5 2 2 2 4 3 2 4;}
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12 /* Style Definitions */
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13 p.MsoNormal, li.MsoNormal, div.MsoNormal
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14 {margin-top:0in;
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15 margin-right:0in;
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16 margin-bottom:10.0pt;
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17 margin-left:0in;
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18 line-height:115%;
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19 font-size:11.0pt;
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20 font-family:"Calibri","sans-serif";}
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21 a:link, span.MsoHyperlink
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22 {color:blue;
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23 text-decoration:underline;}
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24 a:visited, span.MsoHyperlinkFollowed
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25 {color:purple;
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26 text-decoration:underline;}
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27 span.apple-converted-space
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28 {mso-style-name:apple-converted-space;}
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29 .MsoChpDefault
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30 {font-family:"Calibri","sans-serif";}
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31 .MsoPapDefault
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32 {margin-bottom:10.0pt;
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33 line-height:115%;}
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34 @page WordSection1
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35 {size:8.5in 11.0in;
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36 margin:1.0in 1.0in 1.0in 1.0in;}
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37 div.WordSection1
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38 {page:WordSection1;}
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39 -->
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40 </style>
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41
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42 </head>
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43
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44 <body lang=EN-US link=blue vlink=purple>
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45
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46 <div class=WordSection1>
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47
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48 <p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB
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49 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
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50 graphs in this tab give insight into the subclass distribution of IGG and IGA
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51 transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
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52 font-family:"Times New Roman","serif"'>Human Cµ, C&#945;, C&#947; and C&#949;
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53 constant genes are assigned using a </span><span lang=EN-GB style='font-size:
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54 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script
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55 specifically designed for human (sub)class assignment in repertoire data as
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56 described in van Schouwenburg and IJspeert et al, submitted for publication. In
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57 this script the reference sequences for the subclasses are divided in 8
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58 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are
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59 then individually aligned in the right order to each input sequence. The
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60 percentage of the chunks identified in each rearrangement is calculated in the
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61 ‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt;
0
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62 line-height:115%;font-family:"Times New Roman","serif"'>C&#945; and C&#947;
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63 subclasses are very homologous and only differ in a few nucleotides. To assign
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64 subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height:
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65 115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated.
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66 This percentage indicates how well the chunks covering the subclass specific
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67 nucleotide match with the different subclasses. </span><span lang=EN-GB
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68 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information
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69 on normal distribution of subclasses in healthy individuals of different ages
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70 can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p>
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71
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72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a
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73 name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB
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74 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA
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75 subclass distribution</span></u></a></p>
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76
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77 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
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78 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie
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79 chart showing the relative distribution of IGA1 and IGA2 transcripts in the
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80 sample.</span></p>
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81
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82 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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83 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG
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84 subclass distribution</span></u></p>
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85
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86 <p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB
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87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie
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88 chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4
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89 transcripts in the sample.</span></p>
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90
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91 </div>
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92
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93 </body>
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94
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95 </html>