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comparison shm_first.htm @ 39:a24f8c93583a draft

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author davidvanzessen
date Thu, 22 Dec 2016 09:39:27 -0500
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38:05c62efdc393 39:a24f8c93583a
1 <html>
2
3 <head>
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
6 <style>
7 <!--
8 /* Font Definitions */
9 @font-face
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32 </style>
33
34 </head>
35
36 <body lang=EN-US>
37
38 <div class=WordSection1>
39
40 <p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt;
41 text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
42 font-family:"Times New Roman","serif"'>Table showing the order of each
43 filtering step and the number and percentage of sequences after each filtering
44 step. </span></p>
45
46 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
47 text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size:
48 12.0pt;font-family:"Times New Roman","serif"'>Input:</span></u><span
49 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The
50 number of sequences in the original IMGT file. This is always 100% of the
51 sequences.</span></p>
52
53 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
54 text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size:
55 12.0pt;font-family:"Times New Roman","serif"'>After &quot;no results&quot; filter: </span></u><span
56 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IMGT
57 classifies sequences either as &quot;productive&quot;, &quot;unproductive&quot;, &quot;unknown&quot;, or &quot;no
58 results&quot;. Here, the number and percentages of sequences that are not classified
59 as &quot;no results&quot; are reported.</span></p>
60
61 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
62 text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size:
63 12.0pt;font-family:"Times New Roman","serif"'>After functionality filter:</span></u><span
64 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The
65 number and percentages of sequences that have passed the functionality filter. The
66 filtering performed is dependent on the settings of the functionality filter.
67 Details on the functionality filter <a name="OLE_LINK12"></a><a
68 name="OLE_LINK11"></a><a name="OLE_LINK10">can be found on the start page of
69 the SHM&amp;CSR pipeline</a>.</span></p>
70
71 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
72 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
73 removal sequences that are missing a gene region:</span></u><span lang=EN-GB
74 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
75 In this step all sequences that are missing a gene region (FR1, CDR1, FR2,
76 CDR2, FR3) that should be present are removed from analysis. The sequence
77 regions that should be present are dependent on the settings of the sequence
78 starts at filter. <a name="OLE_LINK9"></a><a name="OLE_LINK8">The number and
79 percentage of sequences that pass this filter step are reported.</a> </span></p>
80
81 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
82 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
83 N filter:</span></u><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
84 font-family:"Times New Roman","serif"'> In this step all sequences that contain
85 an ambiguous base (n) in the analysed region or the CDR3 are removed from the
86 analysis. The analysed region is determined by the setting of the sequence
87 starts at filter. The number and percentage of sequences that pass this filter
88 step are reported.</span></p>
89
90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
92 filter unique sequences</span></u><span lang=EN-GB style='font-size:12.0pt;
93 line-height:115%;font-family:"Times New Roman","serif"'>: The number and
94 percentage of sequences that pass the &quot;filter unique sequences&quot; filter. Details
95 on this filter </span><span lang=EN-GB style='font-size:12.0pt;line-height:
96 115%;font-family:"Times New Roman","serif"'>can be found on the start page of
97 the SHM&amp;CSR pipeline</span></p>
98
99 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
100 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>After
101 remove duplicate based on filter:</span></u><span lang=EN-GB style='font-size:
102 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> The number and
103 percentage of sequences that passed the remove duplicate filter. Details on the
104 &quot;remove duplicate filter based on filter&quot; can be found on the start page of the
105 SHM&amp;CSR pipeline.</span></p>
106
107 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK17"></a><a
108 name="OLE_LINK16"><u><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
109 font-family:"Times New Roman","serif"'>Number of matches sequences:</span></u></a><span
110 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
111 The number and percentage of sequences that passed all the filters described
112 above and have a (sub)class assigned.</span></p>
113
114 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
115 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Number
116 of unmatched sequences</span></u><span lang=EN-GB style='font-size:12.0pt;
117 line-height:115%;font-family:"Times New Roman","serif"'>: The number and percentage
118 of sequences that passed all the filters described above and do not have
119 subclass assigned.</span></p>
120
121 <p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
122
123 </div>
124
125 </body>
126
127 </html>