Mercurial > repos > davidvanzessen > shm_csr
diff shm_csr.htm @ 83:729738462297 draft
"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
| author | rhpvorderman |
|---|---|
| date | Wed, 15 Sep 2021 12:24:06 +0000 |
| parents | ba33b94637ca |
| children | 6809c63d9161 |
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--- a/shm_csr.htm Thu Feb 25 10:32:32 2021 +0000 +++ b/shm_csr.htm Wed Sep 15 12:24:06 2021 +0000 @@ -1,95 +1,95 @@ -<html> - -<head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> -<meta name=Generator content="Microsoft Word 14 (filtered)"> -<style> -<!-- - /* Font Definitions */ - @font-face - {font-family:Calibri; - panose-1:2 15 5 2 2 2 4 3 2 4;} - /* Style Definitions */ - p.MsoNormal, li.MsoNormal, div.MsoNormal - {margin-top:0in; - margin-right:0in; - margin-bottom:10.0pt; - margin-left:0in; - line-height:115%; - font-size:11.0pt; - font-family:"Calibri","sans-serif";} -a:link, span.MsoHyperlink - {color:blue; - text-decoration:underline;} -a:visited, span.MsoHyperlinkFollowed - {color:purple; - text-decoration:underline;} -span.apple-converted-space - {mso-style-name:apple-converted-space;} -.MsoChpDefault - {font-family:"Calibri","sans-serif";} -.MsoPapDefault - {margin-bottom:10.0pt; - line-height:115%;} -@page WordSection1 - {size:8.5in 11.0in; - margin:1.0in 1.0in 1.0in 1.0in;} -div.WordSection1 - {page:WordSection1;} ---> -</style> - -</head> - -<body lang=EN-US link=blue vlink=purple> - -<div class=WordSection1> - -<p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The -graphs in this tab give insight into the subclass distribution of IGG and IGA -transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%; -font-family:"Times New Roman","serif"'>Human Cµ, Cα, Cγ and Cε -constant genes are assigned using a </span><span lang=EN-GB style='font-size: -12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script -specifically designed for human (sub)class assignment in repertoire data as -described in van Schouwenburg and IJspeert et al, submitted for publication. In -this script the reference sequences for the subclasses are divided in 8 -nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are -then individually aligned in the right order to each input sequence. The -percentage of the chunks identified in each rearrangement is calculated in the -‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt; -line-height:115%;font-family:"Times New Roman","serif"'>Cα and Cγ -subclasses are very homologous and only differ in a few nucleotides. To assign -subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height: -115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. -This percentage indicates how well the chunks covering the subclass specific -nucleotide match with the different subclasses. </span><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information -on normal distribution of subclasses in healthy individuals of different ages -can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p> - -<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a -name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA -subclass distribution</span></u></a></p> - -<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie -chart showing the relative distribution of IGA1 and IGA2 transcripts in the -sample.</span></p> - -<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG -subclass distribution</span></u></p> - -<p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie -chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4 -transcripts in the sample.</span></p> - -</div> - -</body> - -</html> +<html> + +<head> +<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta name=Generator content="Microsoft Word 14 (filtered)"> +<style> +<!-- + /* Font Definitions */ + @font-face + {font-family:Calibri; + panose-1:2 15 5 2 2 2 4 3 2 4;} + /* Style Definitions */ + p.MsoNormal, li.MsoNormal, div.MsoNormal + {margin-top:0in; + margin-right:0in; + margin-bottom:10.0pt; + margin-left:0in; + line-height:115%; + font-size:11.0pt; + font-family:"Calibri","sans-serif";} +a:link, span.MsoHyperlink + {color:blue; + text-decoration:underline;} +a:visited, span.MsoHyperlinkFollowed + {color:purple; + text-decoration:underline;} +span.apple-converted-space + {mso-style-name:apple-converted-space;} +.MsoChpDefault + {font-family:"Calibri","sans-serif";} +.MsoPapDefault + {margin-bottom:10.0pt; + line-height:115%;} +@page WordSection1 + {size:8.5in 11.0in; + margin:1.0in 1.0in 1.0in 1.0in;} +div.WordSection1 + {page:WordSection1;} +--> +</style> + +</head> + +<body lang=EN-US link=blue vlink=purple> + +<div class=WordSection1> + +<p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The +graphs in this tab give insight into the subclass distribution of IGG and IGA +transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%; +font-family:"Times New Roman","serif"'>Human Cµ, Cα, Cγ and Cε +constant genes are assigned using a </span><span lang=EN-GB style='font-size: +12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script +specifically designed for human (sub)class assignment in repertoire data as +described in van Schouwenburg and IJspeert et al, submitted for publication. In +this script the reference sequences for the subclasses are divided in 8 +nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are +then individually aligned in the right order to each input sequence. The +percentage of the chunks identified in each rearrangement is calculated in the +‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt; +line-height:115%;font-family:"Times New Roman","serif"'>Cα and Cγ +subclasses are very homologous and only differ in a few nucleotides. To assign +subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height: +115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. +This percentage indicates how well the chunks covering the subclass specific +nucleotide match with the different subclasses. </span><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information +on normal distribution of subclasses in healthy individuals of different ages +can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a +name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA +subclass distribution</span></u></a></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie +chart showing the relative distribution of IGA1 and IGA2 transcripts in the +sample.</span></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG +subclass distribution</span></u></p> + +<p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie +chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4 +transcripts in the sample.</span></p> + +</div> + +</body> + +</html>