Mercurial > repos > davidvanzessen > argalaxy_tools

view report_clonality/naive_downloads.htm @ 57:33412e85e669 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
author rhpvorderman
date Wed, 02 Feb 2022 10:50:01 +0000
parents 81b3eb11ed2c
children 4c6df851e262
line wrap: on
line source

<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";}
.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'><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
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'><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>

<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></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.<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.<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
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'><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
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'><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"'>The
data used to generate the VD circus plots for “donor name”:</span></u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
Downloads the data set used for the generation of the VD heatmap. For each
uploaded donor a separate download is generated.</span></p>

<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
data used to generate the VJ circus plots for “donor name”:</span></u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
Downloads the data set used for the generation of the VJ heatmap. For each
uploaded donor a separate download is generated.</span></p>

<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
data used to generate the DJ circus plots for “sample name”:</span></u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
Downloads the data set used for the generation of the DJ heatmap. For each
uploaded donor a separate download is generated.</span></p>

<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p>

<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
dataset used to calculate clonality score: </span></u><span style='font-size:
12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
download information on V D and J gene usage, the junctions and the amino acid
sequence of the sequences that passed the chosen filter settings. Note: this
file contains all the replicate sequences form the different input files.</span></p>

<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences
that are present in more than one replicate:</span></u><span style='font-size:
12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to
download a table containing all the sequences that were present in more than
one replicate. It provides the concidence type, clonaltype, sequence name,
replicate number, and the nucleotide sequence</span></p>

<p class=MsoNormal>&nbsp;</p>

</div>

</body>

</html>