diff report_clonality/naive_downloads.htm @ 27:b539aeb75980 draft

Uploaded

--- a/report_clonality/naive_downloads.htm	Mon Feb 13 09:08:46 2017 -0500
+++ b/report_clonality/naive_downloads.htm	Tue Feb 28 08:10:34 2017 -0500
@@ -18,11 +18,6 @@
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-p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
-	{margin:0in;
-	margin-bottom:.0001pt;
-	font-size:11.0pt;
-	font-family:"Calibri","sans-serif";}
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@@ -42,7 +37,14 @@
 
 <div class=WordSection1>
 
-<p class=MsoNormalCxSpFirst style='text-align:justify'><u><span
+<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
@@ -51,27 +53,16 @@
 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='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>
+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;
@@ -86,8 +77,7 @@
 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>
+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
@@ -95,14 +85,32 @@
 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>
+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.</span></p>
+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
@@ -113,6 +121,9 @@
 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
@@ -129,17 +140,53 @@
 
 <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 “donor name”:</span></u><span
+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"'>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>
+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>