Mercurial > repos > davidvanzessen > shm_csr
annotate shm_first.htm @ 93:8fcf31272f6e draft
planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
| author | rhpvorderman |
|---|---|
| date | Mon, 06 Mar 2023 11:36:32 +0000 |
| parents | 6809c63d9161 |
| children |
| rev | line source |
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| 67 | 1 <html> |
| 2 | |
| 3 <head> | |
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6809c63d9161
"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
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67
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4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> |
| 67 | 5 <meta name=Generator content="Microsoft Word 14 (filtered)"> |
| 6 <style> | |
| 7 <!-- | |
| 8 /* Font Definitions */ | |
| 9 @font-face | |
| 10 {font-family:Calibri; | |
| 11 panose-1:2 15 5 2 2 2 4 3 2 4;} | |
| 12 /* Style Definitions */ | |
| 13 p.MsoNormal, li.MsoNormal, div.MsoNormal | |
| 14 {margin-top:0in; | |
| 15 margin-right:0in; | |
| 16 margin-bottom:10.0pt; | |
| 17 margin-left:0in; | |
| 18 line-height:115%; | |
| 19 font-size:11.0pt; | |
| 20 font-family:"Calibri","sans-serif";} | |
| 21 .MsoChpDefault | |
| 22 {font-family:"Calibri","sans-serif";} | |
| 23 .MsoPapDefault | |
| 24 {margin-bottom:10.0pt; | |
| 25 line-height:115%;} | |
| 26 @page WordSection1 | |
| 27 {size:8.5in 11.0in; | |
| 28 margin:1.0in 1.0in 1.0in 1.0in;} | |
| 29 div.WordSection1 | |
| 30 {page:WordSection1;} | |
| 31 --> | |
| 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 "no results" 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 "productive", "unproductive", "unknown", or "no | |
| 58 results". Here, the number and percentages of sequences that are not classified | |
| 59 as "no results" 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&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 "filter unique sequences" 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&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 "remove duplicate filter based on filter" can be found on the start page of the | |
| 105 SHM&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> </span></p> | |
| 122 | |
| 123 </div> | |
| 124 | |
| 125 </body> | |
| 126 | |
| 127 </html> |