Mercurial > repos > davidvanzessen > argalaxy_tools

annotate report_clonality/naive_clonality.htm @ 56:7ae6b6b5d890 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
author rhpvorderman
date Tue, 14 Dec 2021 12:45:47 +0000
parents 81b3eb11ed2c
children 4c6df851e262
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
54
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
1 <html>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
2
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
3 <head>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
6 <style>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
7 <!--
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
8 /* Font Definitions */
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
9 @font-face
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
10 {font-family:Calibri;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
11 panose-1:2 15 5 2 2 2 4 3 2 4;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
12 /* Style Definitions */
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
13 p.MsoNormal, li.MsoNormal, div.MsoNormal
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
14 {margin-top:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
15 margin-right:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
16 margin-bottom:10.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
17 margin-left:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
18 line-height:115%;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
19 font-size:11.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
20 font-family:"Calibri","sans-serif";}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
21 p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
22 {margin:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
23 margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
24 font-size:11.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
25 font-family:"Calibri","sans-serif";}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
26 .MsoChpDefault
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
27 {font-family:"Calibri","sans-serif";}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
28 .MsoPapDefault
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
29 {margin-bottom:10.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
30 line-height:115%;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
31 @page WordSection1
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
32 {size:8.5in 11.0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
33 margin:1.0in 1.0in 1.0in 1.0in;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
34 div.WordSection1
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
35 {page:WordSection1;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
36 -->
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
37 </style>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
38
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
39 </head>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
40
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
41 <body lang=EN-US>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
42
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
43 <div class=WordSection1>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
44
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
45 <p class=MsoNoSpacingCxSpFirst style='text-align:justify'><span
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
46 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>For each donor a
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
47 subtab is provided containing information on the sequence overlap between
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
48 replicates of the different replicates of one donor. Dependent on the settings
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
49 of the Shared clonal types / clonality filter a clonality score is given.  The clonality
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
50 score  is calculated according to the formula described by </span><a
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
51 name="OLE_LINK13"></a><a name="OLE_LINK12"></a><a name="OLE_LINK11"><span
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
52 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Boyd
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
53 et al, PMID: 20161664. </span></a></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
54
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
55 <p class=MsoNoSpacingCxSpLast style='text-align:justify'><span lang=EN-GB
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
56 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>For each
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
57 individual replicate the number of reads is reported. In addition, the number
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
58 of coincidences between the different replicates of the same donor are reported.
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
59 </span></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
60
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
61 <p class=MsoNormal>&nbsp;</p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
62
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
63 </div>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
64
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
65 </body>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
66
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
67 </html>