Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 27:b539aeb75980 draft
Uploaded
author | davidvanzessen |
---|---|
date | Tue, 28 Feb 2017 08:10:34 -0500 (2017-02-28) |
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(-) [+] |
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--- 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%; 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 @@ -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; + mso-style-unhide:no; + mso-style-qformat:yes; + margin:0in; + margin-bottom:.0001pt; + mso-pagination:widow-orphan; + font-size:11.0pt; + 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; 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 @@ -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> </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 @@ -<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="Gene%20frequencies%20tab_files/filelist.xml"> +<link rel=themeData href="Gene%20frequencies%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; 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-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> </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> </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> </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> </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> </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; 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+ mso-bidi-font-family:"Times New Roman";} +p.msochpdefault, li.msochpdefault, div.msochpdefault + {mso-style-name:msochpdefault; + mso-style-unhide:no; + mso-margin-top-alt:auto; + margin-right:0in; + mso-margin-bottom-alt:auto; + margin-left:0in; + mso-pagination:widow-orphan; + font-size:12.0pt; + 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.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; + mso-default-props:yes; + font-size:10.0pt; + mso-ansi-font-size:10.0pt; + mso-bidi-font-size:10.0pt; + font-family:"Calibri","sans-serif"; + mso-ascii-font-family:Calibri; + 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> </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