Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 27:b539aeb75980 draft

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Uploaded
author davidvanzessen
date Tue, 28 Feb 2017 08:10:34 -0500
parents 28fbbdfd7a87
children 798b62942b4b
files report_clonality/naive_cdr3_char.htm report_clonality/naive_downloads.htm report_clonality/naive_gene_freq.htm report_clonality/naive_junction.htm report_clonality/r_wrapper.sh
diffstat 5 files changed, 428 insertions(+), 154 deletions(-) [+]
line wrap: on
line diff
--- a/report_clonality/naive_cdr3_char.htm	Mon Feb 13 09:08:46 2017 -0500
+++ b/report_clonality/naive_cdr3_char.htm	Tue Feb 28 08:10:34 2017 -0500
@@ -18,11 +18,6 @@
 	line-height:115%;
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 	{font-family:"Calibri","sans-serif";}
 .MsoPapDefault
@@ -33,6 +28,18 @@
 	margin:1.0in 1.0in 1.0in 1.0in;}
 div.WordSection1
 	{page:WordSection1;}
+p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
+	{mso-style-priority:1;
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+	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>
 
@@ -43,6 +50,10 @@
 <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>
@@ -51,21 +62,20 @@
 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=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+<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=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+<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=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+<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
@@ -74,19 +84,10 @@
 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'><u><span style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'>D reading frame</span></u></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"'>Bar graph visualizing the frequency by
-which each D reading frame is used in each donor.</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=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+<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>
--- 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 @@
 	line-height:115%;
 	font-size:11.0pt;
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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>
 
--- a/report_clonality/naive_gene_freq.htm	Mon Feb 13 09:08:46 2017 -0500
+++ b/report_clonality/naive_gene_freq.htm	Tue Feb 28 08:10:34 2017 -0500
@@ -1,103 +1,217 @@
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-<body lang=EN-US>
+<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"'>This tab gives information on the
-frequency of V, D and J gene usage. </span></p>
+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=MsoNoSpacingCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Graphs</span></b></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=MsoNormalCxSpFirst 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"'>Distribution of V gene families</span></u></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=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
-text-align:justify;line-height:normal'><a name="OLE_LINK123"></a><a
-name="OLE_LINK122"></a><a name="OLE_LINK121"><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'>Bar graph showing the frequency
-of V gene family usage in all uploaded donors. </span></a></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=MsoNormalCxSpMiddle 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"'>Relative frequency of V gene
-usage</span></u></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=MsoNormalCxSpLast style='margin-bottom:0in;margin-bottom:.0001pt;
-text-align:justify;line-height:normal'><a name="OLE_LINK126"></a><a
-name="OLE_LINK125"></a><a name="OLE_LINK124"><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'>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></a></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=MsoNoSpacingCxSpLast style='text-align:justify'><a name="OLE_LINK129"></a><a
-name="OLE_LINK128"></a><a name="OLE_LINK127"><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Relative
-frequency of D gene usage</span></u></a></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=MsoNormalCxSpFirst 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 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.</span></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'>Relative
+frequency of J gene usage<o:p></o:p></span></u></p>
 
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Relative
-frequency of J gene usage</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=MsoNormalCxSpFirst 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 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.</span></span></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>
 
--- a/report_clonality/naive_junction.htm	Mon Feb 13 09:08:46 2017 -0500
+++ b/report_clonality/naive_junction.htm	Tue Feb 28 08:10:34 2017 -0500
@@ -1,89 +1,201 @@
-<html>
+<html xmlns:v="urn:schemas-microsoft-com:vml"
+xmlns:o="urn:schemas-microsoft-com:office:office"
+xmlns:w="urn:schemas-microsoft-com:office:word"
+xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
+xmlns="http://www.w3.org/TR/REC-html40">
 
 <head>
 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
+<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="Junction%20analysis%20tab_files/filelist.xml">
+<link rel=themeData href="Junction%20analysis%20tab_files/themedata.thmx">
 <style>
 <!--
  /* Font Definitions */
  @font-face
 	{font-family:Calibri;
-	panose-1:2 15 5 2 2 2 4 3 2 4;}
+	panose-1:2 15 5 2 2 2 4 3 2 4;
+	mso-font-charset:0;
+	mso-generic-font-family:swiss;
+	mso-font-pitch:variable;
+	mso-font-signature:-536870145 1073786111 1 0 415 0;}
  /* Style Definitions */
  p.MsoNormal, li.MsoNormal, div.MsoNormal
-	{margin-top:0in;
+	{mso-style-unhide:no;
+	mso-style-qformat:yes;
+	mso-style-parent:"";
+	margin-top:0in;
 	margin-right:0in;
 	margin-bottom:10.0pt;
 	margin-left:0in;
 	line-height:115%;
+	mso-pagination:widow-orphan;
 	font-size:11.0pt;
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+	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.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
-	{margin:0in;
+	{mso-style-priority:1;
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+	mso-style-qformat:yes;
+	margin:0in;
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+	font-family:"Calibri","sans-serif";
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+	mso-fareast-theme-font:minor-fareast;
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+p.msochpdefault, li.msochpdefault, div.msochpdefault
+	{mso-style-name:msochpdefault;
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+	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;}
+span.GramE
+	{mso-style-name:"";
+	mso-gram-e:yes;}
 .MsoChpDefault
-	{font-family:"Calibri","sans-serif";}
+	{mso-style-type:export-only;
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+	mso-hansi-font-family:Calibri;}
 .MsoPapDefault
-	{margin-bottom:10.0pt;
+	{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;}
+	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>
+<body lang=EN-US style='tab-interval:.5in'>
 
 <div class=WordSection1>
 
-<p class=MsoNormalCxSpFirst 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'><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=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Productive
-mean table</span></u></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=MsoNormalCxSpMiddle style='text-align:justify'><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. 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 mean
+tables<o:p></o:p></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"'>Unproductive
-mean table</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=MsoNormalCxSpMiddle style='text-align:justify'><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. For explanation about the different deletions
-and N and P nucleotides see figure above. </span></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=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Productive
-median table</span></u></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=MsoNormalCxSpMiddle style='text-align:justify'><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. For explanation about the different deletions
-and N and P nucleotides see figure above. </span></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=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Unproductive
-median table</span></u></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=MsoNormalCxSpMiddle style='text-align:justify'><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. For explanation about the different deletions
-and N and P nucleotides see figure above. </span></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>
 
--- a/report_clonality/r_wrapper.sh	Mon Feb 13 09:08:46 2017 -0500
+++ b/report_clonality/r_wrapper.sh	Tue Feb 28 08:10:34 2017 -0500
@@ -325,7 +325,7 @@
 	echo "<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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
 	do
-		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-/td></tr>" >> $outputFile
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_median_nD.txt
 	echo "</tbody></table>" >> $outputFile