Mercurial > repos > davidvanzessen > shm_csr
diff shm_first.htm @ 83:729738462297 draft
"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
| author | rhpvorderman |
|---|---|
| date | Wed, 15 Sep 2021 12:24:06 +0000 |
| parents | ba33b94637ca |
| children | 6809c63d9161 |
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--- a/shm_first.htm Thu Feb 25 10:32:32 2021 +0000 +++ b/shm_first.htm Wed Sep 15 12:24:06 2021 +0000 @@ -1,127 +1,127 @@ -<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='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif"'>Table showing the order of each -filtering step and the number and percentage of sequences after each filtering -step. </span></p> - -<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>Input:</span></u><span -lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The -number of sequences in the original IMGT file. This is always 100% of the -sequences.</span></p> - -<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>After "no results" filter: </span></u><span -lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IMGT -classifies sequences either as "productive", "unproductive", "unknown", or "no -results". Here, the number and percentages of sequences that are not classified -as "no results" are reported.</span></p> - -<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>After functionality filter:</span></u><span -lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The -number and percentages of sequences that have passed the functionality filter. The -filtering performed is dependent on the settings of the functionality filter. -Details on the functionality filter <a name="OLE_LINK12"></a><a -name="OLE_LINK11"></a><a name="OLE_LINK10">can be found on the start page of -the SHM&CSR pipeline</a>.</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"'>After -removal sequences that are missing a gene region:</span></u><span lang=EN-GB -style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> -In this step all sequences that are missing a gene region (FR1, CDR1, FR2, -CDR2, FR3) that should be present are removed from analysis. The sequence -regions that should be present are dependent on the settings of the sequence -starts at filter. <a name="OLE_LINK9"></a><a name="OLE_LINK8">The number and -percentage of sequences that pass this filter step are reported.</a> </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"'>After -N filter:</span></u><span lang=EN-GB style='font-size:12.0pt;line-height:115%; -font-family:"Times New Roman","serif"'> In this step all sequences that contain -an ambiguous base (n) in the analysed region or the CDR3 are removed from the -analysis. The analysed region is determined by the setting of the sequence -starts at filter. The number and percentage of sequences that pass this filter -step are reported.</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"'>After -filter unique sequences</span></u><span lang=EN-GB style='font-size:12.0pt; -line-height:115%;font-family:"Times New Roman","serif"'>: The number and -percentage of sequences that pass the "filter unique sequences" filter. Details -on this filter </span><span lang=EN-GB style='font-size:12.0pt;line-height: -115%;font-family:"Times New Roman","serif"'>can be found on the start page of -the SHM&CSR pipeline</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"'>After -remove duplicate based on filter:</span></u><span lang=EN-GB style='font-size: -12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> The number and -percentage of sequences that passed the remove duplicate filter. Details on the -"remove duplicate filter based on filter" can be found on the start page of the -SHM&CSR pipeline.</span></p> - -<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK17"></a><a -name="OLE_LINK16"><u><span lang=EN-GB style='font-size:12.0pt;line-height:115%; -font-family:"Times New Roman","serif"'>Number of matches sequences:</span></u></a><span -lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> -The number and percentage of sequences that passed all the filters described -above and have a (sub)class assigned.</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"'>Number -of unmatched sequences</span></u><span lang=EN-GB style='font-size:12.0pt; -line-height:115%;font-family:"Times New Roman","serif"'>: The number and percentage -of sequences that passed all the filters described above and do not have -subclass assigned.</span></p> - -<p class=MsoNormal><span lang=EN-GB> </span></p> - -</div> - -</body> - -</html> +<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='margin-bottom:0in;margin-bottom:.0001pt; +text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif"'>Table showing the order of each +filtering step and the number and percentage of sequences after each filtering +step. </span></p> + +<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; +text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: +12.0pt;font-family:"Times New Roman","serif"'>Input:</span></u><span +lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The +number of sequences in the original IMGT file. This is always 100% of the +sequences.</span></p> + +<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; +text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: +12.0pt;font-family:"Times New Roman","serif"'>After "no results" filter: </span></u><span +lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IMGT +classifies sequences either as "productive", "unproductive", "unknown", or "no +results". Here, the number and percentages of sequences that are not classified +as "no results" are reported.</span></p> + +<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; +text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: +12.0pt;font-family:"Times New Roman","serif"'>After functionality filter:</span></u><span +lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The +number and percentages of sequences that have passed the functionality filter. The +filtering performed is dependent on the settings of the functionality filter. +Details on the functionality filter <a name="OLE_LINK12"></a><a +name="OLE_LINK11"></a><a name="OLE_LINK10">can be found on the start page of +the SHM&CSR pipeline</a>.</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"'>After +removal sequences that are missing a gene region:</span></u><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> +In this step all sequences that are missing a gene region (FR1, CDR1, FR2, +CDR2, FR3) that should be present are removed from analysis. The sequence +regions that should be present are dependent on the settings of the sequence +starts at filter. <a name="OLE_LINK9"></a><a name="OLE_LINK8">The number and +percentage of sequences that pass this filter step are reported.</a> </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"'>After +N filter:</span></u><span lang=EN-GB style='font-size:12.0pt;line-height:115%; +font-family:"Times New Roman","serif"'> In this step all sequences that contain +an ambiguous base (n) in the analysed region or the CDR3 are removed from the +analysis. The analysed region is determined by the setting of the sequence +starts at filter. The number and percentage of sequences that pass this filter +step are reported.</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"'>After +filter unique sequences</span></u><span lang=EN-GB style='font-size:12.0pt; +line-height:115%;font-family:"Times New Roman","serif"'>: The number and +percentage of sequences that pass the "filter unique sequences" filter. Details +on this filter </span><span lang=EN-GB style='font-size:12.0pt;line-height: +115%;font-family:"Times New Roman","serif"'>can be found on the start page of +the SHM&CSR pipeline</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"'>After +remove duplicate based on filter:</span></u><span lang=EN-GB style='font-size: +12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> The number and +percentage of sequences that passed the remove duplicate filter. Details on the +"remove duplicate filter based on filter" can be found on the start page of the +SHM&CSR pipeline.</span></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK17"></a><a +name="OLE_LINK16"><u><span lang=EN-GB style='font-size:12.0pt;line-height:115%; +font-family:"Times New Roman","serif"'>Number of matches sequences:</span></u></a><span +lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> +The number and percentage of sequences that passed all the filters described +above and have a (sub)class assigned.</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"'>Number +of unmatched sequences</span></u><span lang=EN-GB style='font-size:12.0pt; +line-height:115%;font-family:"Times New Roman","serif"'>: The number and percentage +of sequences that passed all the filters described above and do not have +subclass assigned.</span></p> + +<p class=MsoNormal><span lang=EN-GB> </span></p> + +</div> + +</body> + +</html>