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diff report_clonality/naive_downloads.htm @ 18:5d11c9139a55 draft

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author davidvanzessen
date Wed, 21 Dec 2016 11:53:03 -0500
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children 3ef457aa5df6
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+<html>
+
+<head>
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+
+<div class=WordSection1>
+
+<p class=MsoNormalCxSpFirst 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'><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='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='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><span lang=EN-GB>.</span><u><span lang=EN-GB style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif"'> </span></u></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. </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.</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'><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'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>A
+frequency count of a clonotype:</span></u><span style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif"'> The frequency count of
+a clonotype in the unfiltered data set. The clonotype defition used is defined
+in the ‘clonal type definition’ filter. </span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>