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date | Wed, 30 Apr 2025 12:44:38 +0000 |
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<html><head><title>Report on: IDNOSPACE </title><script type='text/javascript' src='jquery-1.11.0.min.js'></script> <link rel='stylesheet' type='text/css' href='pure-min.css'> <script type='text/javascript' src='tabber.js'></script> <script type='text/javascript' src='script.js'></script> <link rel='stylesheet' type='text/css' href='style.css'></head> <div class='tabber'><div class='tabbertab' title='Gene frequencies'> <a href='VFPlot.pdf'><img src='VFPlot.png'/></a> <a href='VPlot.pdf'><img src='VPlot.png'/></a> <a href='JPlot.pdf'><img src='JPlot.png'/></a> <br /> <a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a> <html> <head> <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=ProgId content=Word.Document> <meta name=Generator content="Microsoft Word 14"> <meta name=Originator content="Microsoft Word 14"> <link rel=File-List href="Gene%20frequencies%20tab_files/filelist.xml"> <link rel=themeData href="Gene%20frequencies%20tab_files/themedata.thmx"> <style> <!-- /* Font Definitions */ @font-face {font-family:Calibri; 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mso-style-unhide:no; mso-margin-top-alt:auto; margin-right:0in; mso-margin-bottom-alt:auto; margin-left:0in; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri","sans-serif"; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-bidi-font-family:"Times New Roman";} p.msopapdefault, li.msopapdefault, div.msopapdefault {mso-style-name:msopapdefault; mso-style-unhide:no; mso-margin-top-alt:auto; margin-right:0in; margin-bottom:10.0pt; margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} .MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-size:10.0pt; mso-ansi-font-size:10.0pt; mso-bidi-font-size:10.0pt; mso-ascii-font-family:Calibri; mso-hansi-font-family:Calibri;} .MsoPapDefault {mso-style-type:export-only; margin-bottom:10.0pt; line-height:115%;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.WordSection1 {page:WordSection1;} --> </style> <!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri","sans-serif";} </style> <![endif]--><!--[if gte mso 9]><xml> <o:shapedefaults v:ext="edit" spidmax="1026"/> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1"/> </o:shapelayout></xml><![endif]--> </head> <body lang=EN-US style='tab-interval:.5in'> <div class=WordSection1> <p class=MsoNoSpacing style='text-align:justify'><b><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: EN-GB'>Gene frequencies tab</span></u></b></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>This tab gives information on the frequency of V, D and J gene usage. <o:p></o:p></span></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><o:p> </o:p></p> <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: EN-GB'>Graphs</span></b></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Distribution of V gene families<o:p></o:p></span></u></p> <p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK121"></a><a name="OLE_LINK123"></a><a name="OLE_LINK122"></a><span style='mso-bookmark: OLE_LINK121'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; mso-ansi-language:EN-GB'>Bar graph showing the frequency of V gene family usage in all uploaded donors. </span></span><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'><o:p></o:p></span></p> <p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative frequency of V gene usage<o:p></o:p></span></u></p> <p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK124"></a><a name="OLE_LINK126"></a><a name="OLE_LINK125"></a><span style='mso-bookmark: OLE_LINK124'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; mso-ansi-language:EN-GB'>Bar graph showing the frequency of V genes in all uploaded donors. The order of the V genes on the x-axis can be altered by altering the “<span style='color:black;background:white'>Order of V(D)J genes in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; color:black;background:white;mso-ansi-language:EN-GB'><o:p></o:p></span></p> <p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative frequency of D gene usage<o:p></o:p></span></u></p> <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: EN-GB'>Bar graph showing the frequency of D genes in all uploaded donors. The order of the D genes on the x-axis can be altered by altering the “<span style='color:black;background:white'>Order of V(D)J genes in graphs” filter on the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> <p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative frequency of J gene usage<o:p></o:p></span></u></p> <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: EN-GB'>Bar graph showing the frequency of J genes in all uploaded donors. The order of the J genes on the x-axis can be altered by altering the “<span style='color:black;background:white'>Order of V(D)J genes in graphs” filter on the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> <p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>D reading frame<o:p></o:p></span></u></p> <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: EN-GB'>Bar graph visualizing the frequency by which each D reading frame is used in each donor.</span></p> </div> </body> </html> </div> <div class='tabbertab' title='CDR3 Characteristics'> <a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br /> <a href='AAComposition.pdf'><img src='AAComposition.png'/></a> <table class='pure-table pure-table-striped'> <thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead> <tr><td>IDNOSPACE</td><td>13</td></tr> </table> <html> <head> <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <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";} .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;} p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing {mso-style-priority:1; mso-style-unhide:no; mso-style-qformat:yes; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-bidi-font-family:"Times New Roman";} --> </style> </head> <body lang=EN-US> <div class=WordSection1> <p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><b><u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>CDR3 characteristics tab</span></u></b></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif"'>This tab gives information on the different characteristics of the CDR3.</span></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><b><span lang=EN-GB style='font-size: 12.0pt;font-family:"Times New Roman","serif"'>Graphs</span></b></p> <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>length distribution of CDR3</span></u></p> <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>Graph visualizing for each donor the distribution of the CDR3 length in amino acids between all sequences.</span></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>Amino acid composition of CDR3</span></u></p> <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif"'>Bar graph visualizing for each donor how frequent each amino acid is used in the CDR3 of all sequences. The red colour in the background indicate positively charged amino acids, and the blue colour in the background indicate negatively charged amino acids. The amino acids are ordered from hydrophilic (left) to hydrophobic (right). </span></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><b><span lang=EN-GB style='font-size: 12.0pt;font-family:"Times New Roman","serif"'>Table</span></b></p> <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif"'>Table showing for each donor the median CDR3 length.</span></p> <p class=MsoNormal><span lang=EN-GB> </span></p> </div> </body> </html> </div> <div class='tabbertab' title='Heatmaps'><div class='tabber'> <div class='tabbertab' title='IDNOSPACE'><table border='1'><tr> <td><a href='HeatmapVJ_IDNOSPACE.pdf'><img src='HeatmapVJ_IDNOSPACE.png'/></a></td> </tr></table></div> <html> <head> <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <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";} p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing {margin:0in; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri","sans-serif";} .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> <div class=WordSection1> <p class=MsoNormalCxSpFirst style='text-align:justify'><span style='font-size: 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>In this tab heatmaps are provided showing the frequency of different combinations V and D, D and J and V and J genes according together. For each donor a subtab with all three heatmaps is provided.</span></p> <p class=MsoNormal> </p> </div> </body> </html> </div></div> <div class='tabbertab' title='Compare Heatmaps'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead> <tr><td>IDNOSPACE</td><td><input type='checkbox' onchange="javascript:compareAdd('IDNOSPACE')" id='compare_checkbox_IDNOSPACE'/></td></tr> </table><div name='comparisonarea'> <table><tr id='comparison_table_vd'></tr></table> <table><tr id='comparison_table_vj'></tr></table> <table><tr id='comparison_table_dj'></tr></table> <html> <head> <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <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";} p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing {margin:0in; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri","sans-serif";} .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> <div class=WordSection1> <p class=MsoNormalCxSpFirst style='text-align:justify'><span style='font-size: 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The tab allows you to compare the VD, VJ and DJ heatmaps of multiple donors to each other. </span></p> <p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family: "Times New Roman","serif"'>By ticking the include box of a donor, the three heatmaps of this donor is visualized underneath eachother. By clicking the include box of multiple replicates the heatmaps of these replicates are visualized next to each other allowing easy comparison of heatmaps. </span></p> <p class=MsoNormal> </p> </div> </body> </html> </div></div> <div class='tabbertab' title='Circos'><div class='tabber'> <div class='tabbertab' title='IDNOSPACE'><table border='1'><center> <tr><td>V-J</td><td><a href='circosVJ_IDNOSPACE.svg'><img src='circosVJ_IDNOSPACE.png' width='700' height='700'/></td></tr> <center></table></div> <html> <head> <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <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";} p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing {margin:0in; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri","sans-serif";} .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> <div class=WordSection1> <p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family: "Times New Roman","serif"'>Martin Krzywinski, Jacqueline Schein, İnanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco A. Marra (2009). Circos: An information aesthetic for comparative genomics. In <i>Genome Research 10.1101/gr.092759.109</i>.</span></p> <p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family: "Times New Roman","serif"'>Circos plot showing the V-D, V-J, and D-J gen usage. The thicker the line the more frequent this gene combination is used.</span></p> </div> </body> </html> </div></div> <div class='tabbertab' title='Junction Analysis'> <img src='IGH_junctie_analyse.png' /> <center><p style='font-size: 20;'>Unique rearrangements with a V, D and J gene assigned</p></center> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>11049</td><td>1.5</td><td>0.2</td><td>5.3</td><td>0.1</td><td>7.2</td><td>5.5</td><td>0.1</td><td>5.6</td><td>0.1</td><td>6.8</td><td>21</td><td>10.9</td><td>0.4</td><td>13</td></tr> </tbody></table> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>2705</td><td>2</td><td>0.2</td><td>7.8</td><td>0.1</td><td>7.1</td><td>4.5</td><td>0</td><td>10</td><td>0</td><td>12.1</td><td>25.7</td><td>17.8</td><td>0.4</td><td>-</td></tr> </tbody></table> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>11049</td><td>1</td><td>0</td><td>4</td><td>0</td><td>6</td><td>4</td><td>0</td><td>5</td><td>0</td><td>6</td><td>21</td><td>10</td><td>0</td><td>13</td></tr> </tbody></table> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>2705</td><td>1</td><td>0</td><td>6</td><td>0</td><td>6</td><td>3</td><td>0</td><td>10</td><td>0</td><td>15</td><td>26</td><td>17</td><td>0</td><td>-</td></tr> </tbody></table> <center><p style='font-size: 20;'>Unique rearrangements with only a V and J gene assigned</p></center> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>98</td><td>1.1</td><td>0.3</td><td>3.2</td><td>0</td><td>4.7</td><td>1.1</td><td>3.2</td><td>0.1</td><td>8</td></tr> </tbody></table> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>89</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>0</td><td>3</td><td>0</td><td>-</td></tr> </tbody></table> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>98</td><td>1</td><td>0</td><td>3</td><td>0</td><td>2.5</td><td>0</td><td>3</td><td>0</td><td>8</td></tr> </tbody></table> <table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody> <tr><td>IDNOSPACE</td><td>89</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>0</td><td>3</td><td>0</td><td>-</td></tr> </tbody></table> <html> <head> <meta http-equiv=Content-Type content="text/html; 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font-size:10.0pt; font-family:"Calibri","sans-serif";} </style> <![endif]--><!--[if gte mso 9]><xml> <o:shapedefaults v:ext="edit" spidmax="1026"/> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1"/> </o:shapelayout></xml><![endif]--> </head> <body lang=EN-US style='tab-interval:.5in'> <div class=WordSection1> <p class=MsoNormal style='text-align:justify'><b><u><span style='font-size: 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Junction analysis tab </span></u></b></p> <p class=MsoNormal style='text-align:justify'><b><span style='font-size:12.0pt; line-height:115%;font-family:"Times New Roman","serif"'>Tables:</span></b></p> <p class=MsoNormal style='text-align:justify'><span style='font-size:12.0pt; line-height:115%;font-family:"Times New Roman","serif"'>The unique rearrangements are separated in sequences that contain <span class=GramE>both a</span> V, D and J gene and sequences that contain only a V and J gene.</span></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Productive mean tables<o:p></o:p></span></u></p> <p class=MsoNormal style='text-align:justify'><span class=GramE><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports for each donor the number of productive sequences and the mean number of deletions, N-nucleotides and P-nucleotides.</span></span><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> For explanation about the different deletions and N and P nucleotides see figure above. </span></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Unproductive mean table<o:p></o:p></span></u></p> <p class=MsoNormal style='text-align:justify'><span class=GramE><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports for each donor the number of unproductive sequences and the mean number of deletions, N-nucleotides and P-nucleotides.</span></span><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> For explanation about the different deletions and N and P nucleotides see figure above. </span></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Productive median table<o:p></o:p></span></u></p> <p class=MsoNormal style='text-align:justify'><span class=GramE><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports for each donor the number of productive sequences and the median number of deletions, N-nucleotides and P-nucleotides.</span></span><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> For explanation about the different deletions and N and P nucleotides see figure above. </span></p> <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Unproductive median table<o:p></o:p></span></u></p> <p class=MsoNormal style='text-align:justify'><span class=GramE><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Reports for each donor the number of unproductive sequences and the median number of deletions, N-nucleotides and P-nucleotides.</span></span><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> For explanation about the different deletions and N and P nucleotides see figure above. </span></p> <p class=MsoNormal> </p> </div> </body> </html> </div> <div class='tabbertab' title='Downloads'> <table class='pure-table pure-table-striped'> <thead><tr><th>Description</th><th>Link</th></tr></thead> <tr><td>All outputs below in a zip file</td><td><a href='all_outputs.zip'>Download</a></td></tr> <tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr> <tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr> <tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr> <tr><td>The dataset used to generate the relative frequency of V gene usage graph</td><td><a href='VFrequency.txt'>Download</a></td></tr> <tr><td>The dataset used to generate the relative frequency of J gene usage graph</td><td><a href='JFrequency.txt'>Download</a></td></tr> <tr><td>The dataset used to generate the relative frequency of the D reading frame graph</td><td><a href='DReadingFrame.txt'>Download</a></td></tr> <tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr> <tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr> <tr><td>The dataset used to generate the Amino Acid Composition in the CDR3 graph</td><td><a href='AAComposition.txt'>Download</a></td></tr> <tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr> <tr><td>The data used to generate the VJ heatmap for IDNOSPACE.</td><td><a href='HeatmapVJ_IDNOSPACE.txt'>Download</a></td></tr> <tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr> <tr><td>The data used to generate the VJ Circos plots for IDNOSPACE.</td><td><a href='IDNOSPACE_VJ_circos.txt'>Download</a></td></tr> <tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr> <tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, none)</td><td><a href='clonalityComplete.txt'>Download</a></td></tr> </table> <html> <head> <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <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";} .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> <div class=WordSection1> <p class=MsoNormalCxSpFirst style='text-align:justify'><b><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads tab</span></u></b></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Description</span></b></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%; font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a name="OLE_LINK14">Allows you to download information on V D and J gene usage, the junctions and the amino acid sequence of the sequences that passed the chosen filter settings. Note: this file contains only 1 sequences of a replicate sequence. </a></span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene frequencies</span></b></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>The dataset used to generate the distribution of V gene families graph:</span></u><span style='font-size:12.0pt;font-family: "Times New Roman","serif"'> Downloads a table with information used to generate the distribution of V gene families graph.</span></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>The dataset used to generate the distribution of D gene families graph: </span></u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>Downloads a table with information used to generate the distribution of D gene families graph.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The dataset used to generate the relative frequency of V gene usage graph:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data used to generate the relative frequency of V gene usage graph. In addition information on the chromosomal order of the V genes can be found.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The dataset used to generate the relative frequency of D gene usage graph:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data used to generate the relative frequency of D gene usage graph. In addition information on the chromosomal order of the D genes can be found.<u> </u></span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The dataset used to generate the relative frequency of J gene usage graph: </span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads the data used to generate the relative frequency of J gene usage graph. In addition information on the chromosomal order of the J genes can be found.<u> </u></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"; color:black'>The dataset used to generate the relative frequency of the D reading frame graph</span></u><span lang=EN-GB style='font-size:12.0pt; line-height:115%;font-family:"Times New Roman","serif";color:black'>: Downloads the data used to generate the relative frequency of the D reading frame. </span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; color:black'>CDR3 characteristics</span></b></p> <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; text-align:justify;line-height:normal'><u><span style='font-size:12.0pt; font-family:"Times New Roman","serif"'>The dataset used to generate the CDR3 length frequency graph:</span></u><span style='font-size:12.0pt;font-family: "Times New Roman","serif"'> Downloads a table with information used for the length distribution of CDR3 plot. </span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the frequency of the different amino acids in the CDR3 of all filtered sequences. This data set is used for the generation of the Amino Acid Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity in included. </span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Heatmaps</span></b></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The data used to generate the VD heatmap for “donor name”:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data set used for the generation of the VD heatmap. For each uploaded donor a separate download is generated.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The data used to generate the VJ heatmap for “donor name”:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data set used for the generation of the VJ heatmap. For each uploaded donor a separate download is generated.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The data used to generate the DJ heatmap for “sample name”:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data set used for the generation of the DJ heatmap. For each uploaded donor a separate download is generated.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Circos</span></b></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The data used to generate the VD circus plots for “donor name”:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data set used for the generation of the VD heatmap. For each uploaded donor a separate download is generated.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The data used to generate the VJ circus plots for “donor name”:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data set used for the generation of the VJ heatmap. For each uploaded donor a separate download is generated.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The data used to generate the DJ circus plots for “sample name”:</span></u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data set used for the generation of the DJ heatmap. For each uploaded donor a separate download is generated.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The dataset used to calculate clonality score: </span></u><span style='font-size: 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to download information on V D and J gene usage, the junctions and the amino acid sequence of the sequences that passed the chosen filter settings. Note: this file contains all the replicate sequences form the different input files.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences that are present in more than one replicate:</span></u><span style='font-size: 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to download a table containing all the sequences that were present in more than one replicate. It provides the concidence type, clonaltype, sequence name, replicate number, and the nucleotide sequence</span></p> <p class=MsoNormal> </p> </div> </body> </html> </div></html>