Mercurial > repos > davidvanzessen > argalaxy_tools
view report_clonality/naive_downloads.htm @ 18:5d11c9139a55 draft
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author | davidvanzessen |
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date | Wed, 21 Dec 2016 11:53:03 -0500 |
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children | 3ef457aa5df6 |
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<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'><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> </p> </div> </body> </html>