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changeset 18:5d11c9139a55 draft

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Uploaded
author davidvanzessen
date Wed, 21 Dec 2016 11:53:03 -0500
parents da95be204ebc
children 3ef457aa5df6
files complete_immunerepertoire.xml report_clonality/RScript.r report_clonality/naive_cdr3_char.htm report_clonality/naive_circos.htm report_clonality/naive_clonality.htm report_clonality/naive_compare.htm report_clonality/naive_downloads.htm report_clonality/naive_gene_freq.htm report_clonality/naive_heatmap.htm report_clonality/naive_junction.htm report_clonality/naive_overview.htm report_clonality/r_wrapper.sh
diffstat 12 files changed, 857 insertions(+), 89 deletions(-) [+]
line wrap: on
line diff
--- a/complete_immunerepertoire.xml	Wed Dec 21 05:57:31 2016 -0500
+++ b/complete_immunerepertoire.xml	Wed Dec 21 11:53:03 2016 -0500
@@ -17,8 +17,8 @@
 	</command>
 	<inputs>
 		<repeat name="patients" title="Donor" min="1" default="1">
-			<repeat name="samples" title="Sample" min="1" default="1">
-					<param name="sample" type="data" label="Sample to Process" />
+			<repeat name="samples" title="Replicate" min="1" default="1">
+					<param name="sample" type="data" label="Replicate to Process" />
 			</repeat>
 			<param name="id" type="text" label="ID" />
 		</repeat>
@@ -118,87 +118,70 @@
 		<!--<requirement type="package" version="0.20">circostools</requirement>-->
 	</requirements>
 	<help>
-		The entire Immune Repertoire pipeline as a single tool, input several FASTA files or IMGT zip/txz files, give them an ID and it will BLAST/parse, merge and plot them.
-
-		.. class:: warningmark
+<![CDATA[
+**References**
 
-Custom gene ordering based on position on genome: 
+Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ (2009). Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. In *Science Translational Medicine 1(12):12ra23*. 
 
-**Human**
+-----
 
-IGH::
+**Input files**
 
-    V:
-    IGHV7-81,IGHV3-74,IGHV3-73,IGHV3-72,IGHV3-71,IGHV2-70,IGHV1-69,IGHV3-66,IGHV3-64,IGHV4-61,IGHV4-59,IGHV1-58,IGHV3-53,IGHV3-52,IGHV5-a,IGHV5-51,IGHV3-49,IGHV3-48,IGHV3-47,IGHV1-46,IGHV1-45,IGHV3-43,IGHV4-39,IGHV3-35,IGHV4-34,IGHV3-33,IGHV4-31,IGHV4-30-4,IGHV4-30-2,IGHV3-30-3,IGHV3-30,IGHV4-28,IGHV2-26,IGHV1-24,IGHV3-23,IGHV3-22,IGHV3-21,IGHV3-20,IGHV3-19,IGHV1-18,IGHV3-15,IGHV3-13,IGHV3-11,IGHV3-9,IGHV1-8,IGHV3-7,IGHV2-5,IGHV7-4-1,IGHV4-4,IGHV4-b,IGHV1-3,IGHV1-2,IGHV6-1
-    D:
-    IGHD1-1,IGHD2-2,IGHD3-3,IGHD6-6,IGHD1-7,IGHD2-8,IGHD3-9,IGHD3-10,IGHD4-11,IGHD5-12,IGHD6-13,IGHD1-14,IGHD2-15,IGHD3-16,IGHD4-17,IGHD5-18,IGHD6-19,IGHD1-20,IGHD2-21,IGHD3-22,IGHD4-23,IGHD5-24,IGHD6-25,IGHD1-26,IGHD7-27
-    J:
-    IGHJ1,IGHJ2,IGHJ3,IGHJ4,IGHJ5,IGHJ6
+IMGT/HighV-QUEST .zip and .txz files and FASTA files are accepted as input files. In addition filtered IMGT files generated using the SHM &amp; CSR pipeline can be used as input files. 
+Note: Files can be uploaded by using “get data” and “upload file”. When uploading IMGT files  “IMGT archive“ should be selected as a file type. When uploading FASTA files the auto-detect function can be used to select a file type. Special characters should be prevented in the file names of the uploaded samples as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
 
+-----
+
+**Donor and replicates**
 
-IGK::
+The immune repertoire pipeline can analyse files from multiple donors in parallel. Therefore for each analysed donor an ID has to be given. This ID can only contain letters, numbers and _. Spaces in the ID give an error when running the immune repertoire pipeline. In the default setting of the immune repertoire pipeline one donor consisting out of one sample can be uploaded. However, multiple samples per donor can be uploaded by using the insert sample button. In addition, multiple donors van be added by using the insert donor button. The multiple sample option can be used when multiple data files from the same donor are available. For the calculation of the clonality score using the algorithm described by Boyd et al (PMID: 20161664) at least 3 samples have to be included per donor. 
+
+-----
 
-    V:
-    IGKV3D-7,IGKV1D-8,IGKV1D-43,IGKV3D-11,IGKV1D-12,IGKV1D-13,IGKV3D-15,IGKV1D-16,IGKV1D-17,IGKV3D-20,IGKV2D-26,IGKV2D-28,IGKV2D-29,IGKV2D-30,IGKV1D-33,IGKV1D-39,IGKV2D-40,IGKV2-40,IGKV1-39,IGKV1-33,IGKV2-30,IGKV2-29,IGKV2-28,IGKV1-27,IGKV2-24,IGKV3-20,IGKV1-17,IGKV1-16,IGKV3-15,IGKV1-13,IGKV1-12,IGKV3-11,IGKV1-9,IGKV1-8,IGKV1-6,IGKV1-5,IGKV5-2,IGKV4-1
-    J:
-    IGKJ1,IGKJ2,IGKJ3,IGKJ4,IGKJ5
+**Clonal Type Definition**
 
+Allows the selection of a single sequence per clone. Different definitions of a clone can be chosen. 
 
-IGL::
+.. class:: infomark
+
+Note: The first sequence (in the data set) of each clone is always included in the analysis. This means that altering the data order (by for instance sorting) can change the sequence which is included in the analysis and therefore slightly influence results. 
 
-    V:
-    IGLV4-69,IGLV8-61,IGLV4-60,IGLV6-57,IGLV5-52,IGLV1-51,IGLV9-49,IGLV1-47,IGLV7-46,IGLV5-45,IGLV1-44,IGLV7-43,IGLV1-41,IGLV1-40,IGLV5-39,IGLV5-37,IGLV1-36,IGLV3-27,IGLV3-25,IGLV2-23,IGLV3-22,IGLV3-21,IGLV3-19,IGLV2-18,IGLV3-16,IGLV2-14,IGLV3-12,IGLV2-11,IGLV3-10,IGLV3-9,IGLV2-8,IGLV4-3,IGLV3-1
-    J:
-    IGLJ1,IGLJ2,IGLJ3,IGLJ6,IGLJ7
+-----
 
-
-TRB::
+**Order of V(D)J genes in graphs**
 
-    V:
-    TRBV2,TRBV3-1,TRBV4-1,TRBV5-1,TRBV6-1,TRBV4-2,TRBV6-2,TRBV4-3,TRBV6-3,TRBV7-2,TRBV6-4,TRBV7-3,TRBV9,TRBV10-1,TRBV11-1,TRBV10-2,TRBV11-2,TRBV6-5,TRBV7-4,TRBV5-4,TRBV6-6,TRBV5-5,TRBV7-6,TRBV5-6,TRBV6-8,TRBV7-7,TRBV6-9,TRBV7-8,TRBV5-8,TRBV7-9,TRBV13,TRBV10-3,TRBV11-3,TRBV12-3,TRBV12-4,TRBV12-5,TRBV14,TRBV15,TRBV16,TRBV18,TRBV19,TRBV20-1,TRBV24-1,TRBV25-1,TRBV27,TRBV28,TRBV29-1,TRBV30
-    D:
-    TRBD1,TRBD2
-    J:
-    TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ1-6,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
+This setting allows you to order the V(D)J genes in the graphs in a user defined order. When using the default “IMGT-DB” all genes in the V, D an J gene graphs will be ordered based on their IMGT numbering. By selecting user defined the order of the V, D and J genes in the graphs can be altered according to the users personal settings. For simplifying of visualizing the genes in the chromosomal order the order of V, D and J genes on the chromosome in are included at the bottom of this help page. For any other ordering please provide the order of gene names divided by commas. 
+
+-----
 
+**Species**
 
-TRA::
+Enter the species of the sample you would like to analyse.
 
-    V:
-    TRAV1-1,TRAV1-2,TRAV2,TRAV3,TRAV4,TRAV5,TRAV6,TRAV7,TRAV8-1,TRAV9-1,TRAV10,TRAV12-1,TRAV8-2,TRAV8-3,TRAV13-1,TRAV12-2,TRAV8-4,TRAV13-2,TRAV14/DV4,TRAV9-2,TRAV12-3,TRAV8-6,TRAV16,TRAV17,TRAV18,TRAV19,TRAV20,TRAV21,TRAV22,TRAV23/DV6,TRAV24,TRAV25,TRAV26-1,TRAV27,TRAV29/DV5,TRAV30,TRAV26-2,TRAV34,TRAV35,TRAV36/DV7,TRAV38-1,TRAV38-2/DV8,TRAV39,TRAV40,TRAV41
-    J:
-    TRAJ57,TRAJ56,TRAJ54,TRAJ53,TRAJ52,TRAJ50,TRAJ49,TRAJ48,TRAJ47,TRAJ46,TRAJ45,TRAJ44,TRAJ43,TRAJ42,TRAJ41,TRAJ40,TRAJ39,TRAJ38,TRAJ37,TRAJ36,TRAJ34,TRAJ33,TRAJ32,TRAJ31,TRAJ30,TRAJ29,TRAJ28,TRAJ27,TRAJ26,TRAJ24,TRAJ23,TRAJ22,TRAJ21,TRAJ20,TRAJ18,TRAJ17,TRAJ16,TRAJ15,TRAJ14,TRAJ13,TRAJ12,TRAJ11,TRAJ10,TRAJ9,TRAJ8,TRAJ7,TRAJ6,TRAJ5,TRAJ4,TRAJ3
+-----
 
+**Locus**
 
-TRG::
+A dropdown menu to select the immune receptor locus to be analysed.
 
-    V:
-    TRGV9,TRGV8,TRGV5,TRGV4,TRGV3,TRGV2
-    J:
-    TRGJ2,TRGJP2,TRGJ1,TRGJP1
+-----
 
+**Remove unproductive sequences from graphs**
 
-TRD::
+This filter provides the option to only include productive sequences or both productive and unproductive sequences in the graphs.
 
-    V:
-    TRDV1,TRDV2,TRDV3
-    D:
-    TRDD1,TRDD2,TRDD3
-    J:
-    TRDJ1,TRDJ4,TRDJ2,TRDJ3
+-----
 
+**Shared clonal types / clonality**
 
-**Mouse**
+This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a sample no sequences overlap or clonality can be determined and therefore the “do not determine overlap” option should be selection. The “Determine the number of sequences that share the same clonal type between the replicates” option allows the user to determine the number of overlapping sequences (based on the clonal type definition defined in the ‘clonal type definition filter’) between different replicates. This can be used to for instance look at different time point in the same donor to changes in the repertoire. When three or more replicates of the same blood same are amplified and sequences in parallel, the “determine clonality of the donor” function can be used to calculate the number of overlapping sequences as well as the clonality score as described by Boyd et al, PMID: 20161664.
 
-TRB::
+-----
 
-    V:
-    TRBV1,TRBV2,TRBV3,TRBV4,TRBV5,TRBV12-1,TRBV13-1,TRBV12-2,TRBV13-2,TRBV13-3,TRBV14,TRBV15,TRBV16,TRBV17,TRBV19,TRBV20,TRBV23,TRBV24,TRBV26,TRBV29,TRBV30,TRBV31
-    D:
-    TRBD1,TRBD2
-    J:
-    TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
-    
+**Execute**
+
+Upon pressing the execute button a new analysis is added to your history (right side of the page). Initially this analysis will be grey, after initiating the analysis colour of the analysis in the history will change to yellow. When the analysis is finished it will turn green in the history. Now the analysis can be opened by clicking on the eye icon on the analysis of interest. When an analysis turns red an error has occurred when running the analysis. If you click on the analysis title additional information can be found on the analysis. In addition a bug icon appears. Here more information on the error can be found.
+]]>
 	</help>
 
 </tool>
--- a/report_clonality/RScript.r	Wed Dec 21 05:57:31 2016 -0500
+++ b/report_clonality/RScript.r	Wed Dec 21 11:53:03 2016 -0500
@@ -159,7 +159,7 @@
 
 #write the complete dataset that is left over, will be the input if 'none' for clonaltype and 'no' for filterproductive
 write.table(PRODF, "allUnique.txt", sep="\t",quote=F,row.names=F,col.names=T)
-write.table(PRODF, "allUnique.csv", sep=",",quote=F,row.names=F,col.names=T)
+#write.table(PRODF, "allUnique.csv", sep=",",quote=F,row.names=F,col.names=T)
 write.table(UNPROD, "allUnproductive.csv", sep=",",quote=F,row.names=F,col.names=T)
 
 #write the samples to a file
@@ -297,7 +297,7 @@
 pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
 pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage") + scale_fill_manual(values=sample.colors)
 pV = pV + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
-write.table(x=PRODFV, file="VFrequency.csv", sep=",",quote=F,row.names=F,col.names=T)
+write.table(x=PRODFV, file="VFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
 png("VPlot.png",width = 1280, height = 720)
 pV
@@ -308,7 +308,7 @@
   pD = pD + geom_bar( aes( x=factor(reorder(Top.D.Gene, chr.orderD)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
   pD = pD + xlab("Summary of D gene") + ylab("Frequency") + ggtitle("Relative frequency of D gene usage") + scale_fill_manual(values=sample.colors)
   pD = pD + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
-  write.table(x=PRODFD, file="DFrequency.csv", sep=",",quote=F,row.names=F,col.names=T)
+  write.table(x=PRODFD, file="DFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T)
   
   png("DPlot.png",width = 800, height = 600)
   print(pD)
@@ -319,7 +319,7 @@
 pJ = pJ + geom_bar( aes( x=factor(reorder(Top.J.Gene, chr.orderJ)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
 pJ = pJ + xlab("Summary of J gene") + ylab("Frequency") + ggtitle("Relative frequency of J gene usage") + scale_fill_manual(values=sample.colors)
 pJ = pJ + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
-write.table(x=PRODFJ, file="JFrequency.csv", sep=",",quote=F,row.names=F,col.names=T)
+write.table(x=PRODFJ, file="JFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
 png("JPlot.png",width = 800, height = 600)
 pJ
@@ -344,7 +344,7 @@
 png("VFPlot.png")
 VPlot
 dev.off();
-write.table(x=VGenes, file="VFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T)
+write.table(x=VGenes, file="VFFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
 if(useD){
   DGenes = PRODF[,c("Sample", "Top.D.Gene")]
@@ -362,7 +362,7 @@
   png("DFPlot.png")
   print(DPlot)
   dev.off();
-  write.table(x=DGenes, file="DFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T)
+  write.table(x=DGenes, file="DFFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T)
 }
 
 # ---------------------- Plotting the cdr3 length ----------------------
@@ -579,7 +579,7 @@
 if("Replicate" %in% colnames(inputdata)) #can only calculate clonality score when replicate information is available
 {
   print("Report Clonality - Clonality")
-  write.table(clonalityFrame, "clonalityComplete.csv", sep=",",quote=F,row.names=F,col.names=T)
+  write.table(clonalityFrame, "clonalityComplete.txt", sep="\t",quote=F,row.names=F,col.names=T)
   if(clonality_method == "boyd"){
     samples = split(clonalityFrame, clonalityFrame$Sample, drop=T)
    
@@ -871,7 +871,7 @@
 png("AAComposition.png",width = 1280, height = 720)
 AAfreqplot
 dev.off()
-write.table(AAfreq, "AAComposition.csv" , sep=",",quote=F,na="-",row.names=F,col.names=T)
+write.table(AAfreq, "AAComposition.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T)
 
 # ---------------------- AA median CDR3 length ----------------------
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_cdr3_char.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,100 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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;
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+@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='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=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"'>length distribution of CDR3</span></u></p>
+
+<p class=MsoNormalCxSpMiddle 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;
+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'><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;
+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>
+
+</div>
+
+</body>
+
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_circos.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,59 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
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+ @font-face
+	{font-family:Calibri;
+	panose-1:2 15 5 2 2 2 4 3 2 4;}
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+
+</head>
+
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+
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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;nan
+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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_clonality.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,67 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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;
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+@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=MsoNoSpacingCxSpFirst style='text-align:justify'><span
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>For each donor a
+subtab is provided containing information on the sequence overlap between
+replicates of the different replicates of one donor. Dependent on the settings
+of the Shared clonal types / clonality filter a clonality score is given. The clonality
+score is calculated according to the formula described by </span><a
+name="OLE_LINK13"></a><a name="OLE_LINK12"></a><a name="OLE_LINK11"><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Boyd
+et al, PMID: 20161664. </span></a></p>
+
+<p class=MsoNoSpacingCxSpLast style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>For each
+individual replicate the number of reads is reported. In addition, the number
+of coincidences between the different replicates of the same donor are reported.
+</span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_compare.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,61 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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 samples the heatmaps of these samples are visualized
+next to each other allowing easy comparison of heatmaps. </span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_downloads.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,150 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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;
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+	{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'><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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_gene_freq.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,106 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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%;}
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+	{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 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>
+
+<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=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=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=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=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=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=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=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=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>
+
+</div>
+
+</body>
+
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_heatmap.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,57 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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";}
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+	{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>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_junction.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,94 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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;
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+	{size:8.5in 11.0in;
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+	{page:WordSection1;}
+-->
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<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=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=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=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=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=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=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=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=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>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/naive_overview.htm	Wed Dec 21 11:53:03 2016 -0500
@@ -0,0 +1,65 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<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='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 the number and percentage of
+(unique) productive and unproductive sequences per sample and per replicate. </span></p>
+
+<p class=MsoNormalCxSpLast 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"'>&nbsp;</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The definition
+of unique sequences is based on the clonal type definition filter setting
+chosen.</span></p>
+
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+
+</div>
+
+</body>
+
+</html>
--- a/report_clonality/r_wrapper.sh	Wed Dec 21 05:57:31 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Wed Dec 21 11:53:03 2016 -0500
@@ -47,7 +47,10 @@
 		echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
 		echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
 done < $outputDir/productive_counting.txt
-echo "</table border></center></html>" >> $2
+echo "</table><br />" >> $2
+echo "Table showing the number and percentage of (unique) productive and unproductive sequences per sample and per replicate. <br />" >> $2
+echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2
+echo "</center></html>" >> $2
 
 echo "<html><head><title>Report on:" >> $outputFile
 
@@ -124,6 +127,9 @@
 	echo "<img src='DPlot.png'/>" >> $outputFile
 fi
 echo "<img src='JPlot.png'/>" >> $outputFile
+
+cat $dir/naive_gene_freq.htm >> $outputFile
+
 echo "</div>" >> $outputFile
 
 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
@@ -139,6 +145,8 @@
 done < $outputDir/AAMedianBySample.csv
 echo "</table>" >> $outputFile
 
+cat $dir/naive_cdr3_char.htm >> $outputFile
+
 echo "</div>" >> $outputFile
 
 #Heatmaps
@@ -157,8 +165,25 @@
 	echo "</tr></table></div>" >> $outputFile
 	count=$((count+1))
 done
+
+cat $dir/naive_heatmap.htm >> $outputFile
+
 echo "</div></div>" >> $outputFile
 
+echo "<div class='tabbertab' title='Compare Heatmaps'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile
+for sample in $samples; do
+	echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
+done
+echo "</table><div name='comparisonarea'>" >> $outputFile
+echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
+echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
+echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
+
+cat $dir/naive_compare.htm >> $outputFile
+
+echo "</div></div>" >> $outputFile
+
+
 #circos
 
 if [[ "$USECIRCOS" == "yes" ]]; then
@@ -176,6 +201,9 @@
 		echo "<center></table></div>" >> $outputFile
 		count=$((count+1))
 	done
+	
+	cat $dir/naive_circos.htm >> $outputFile
+	
 	echo "</div></div>" >> $outputFile
 fi
 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
@@ -239,6 +267,9 @@
 			echo "</table></div>" >> $outputFile
 		fi
 	done
+	
+	cat $dir/naive_clonality.htm >> $outputFile
+	
 	echo "</div></div>" >> $outputFile
 fi
 
@@ -249,66 +280,58 @@
 	echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
 	echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisProd_mean.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_mean.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisProd_median.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_median.csv
 	echo "</tbody></table>" >> $outputFile
 	
+	cat $dir/naive_junction.htm >> $outputFile
+	
 	echo "</div>" >> $outputFile
 fi
 
-echo "<div class='tabbertab' title='Comparison'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile
-for sample in $samples; do
-	echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
-done
-echo "</table><div name='comparisonarea'>" >> $outputFile
-echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
-echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
-echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
-echo "</div></div>" >> $outputFile
-
 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
-echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile
-echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.txt'>Download</a></td></tr>" >> $outputFile
 
 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
 
-echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>" >> $outputFile
 if [[ "$useD" == "true" ]] ; then
-	echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile
+	echo "<tr><td>The dataset used to generate  the distribution of D gene families graph</td><td><a href='DFFrequency.txt'>Download</a></td></tr>" >> $outputFile
 fi
 
-echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
+echo "<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>" >> $outputFile
 if [[ "$useD" == "true" ]] ; then
-	echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
+	echo "<tr><td>The dataset used to generate the relative frequency of D gene usage graph</td><td><a href='DFrequency.txt'>Download</a></td></tr>" >> $outputFile
 fi
-echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
-echo "<tr><td>The dataset used to generate the AA composition graph</td><td><a href='AAComposition.csv'>Download</a></td></tr>" >> $outputFile
+echo "<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>" >> $outputFile
+echo "<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>" >> $outputFile
 
 for sample in $samples; do
 	if [[ "$useD" == "true" ]] ; then
@@ -323,4 +346,7 @@
 echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile
 
 echo "</table>" >> $outputFile
+
+cat $dir/naive_downloads.htm >> $outputFile
+
 echo "</div></html>" >> $outputFile