Mercurial > repos > davidvanzessen > argalaxy_tools

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<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>
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<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>&nbsp;</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>&nbsp;</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>&nbsp;</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>&nbsp;</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>&nbsp;</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>
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<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>

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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>

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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>&nbsp;</span></p>

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</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>
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<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>&nbsp;</p>

</div>

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</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>
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<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>&nbsp;</p>

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<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>
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<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family:
"Times New Roman","serif"'>Martin Krzywinski, Jacqueline Schein, &#304;nanç
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>

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</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>
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<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>

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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>&nbsp;</p>

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<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>
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<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>&nbsp;</p>

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author	rhpvorderman
date	Wed, 30 Apr 2025 12:44:38 +0000
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