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author davidvanzessen
date Thu, 22 Dec 2016 09:39:27 -0500
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+++ b/shm_clonality.htm	Thu Dec 22 09:39:27 2016 -0500
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+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><b><span lang=EN-GB style='color:black'>References</span></b></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><span lang=EN-GB style='color:black'>Gupta,
+Namita T. and Vander Heiden, Jason A. and Uduman, Mohamed and Gadala-Maria,
+Daniel and Yaari, Gur and Kleinstein, Steven H. (2015). <a name="OLE_LINK106"></a><a
+name="OLE_LINK107"></a>Change-O: a toolkit for analyzing large-scale B cell
+immunoglobulin repertoire sequencing data: Table 1. In<span
+class=apple-converted-space>&nbsp;</span><em>Bioinformatics, 31 (20), pp.
+3356–3358.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><a
+href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
+lang=EN-GB style='color:#303030'>doi:10.1093/bioinformatics/btv359</span></a><span
+lang=EN-GB style='color:black'>][</span><a
+href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
+lang=EN-GB style='color:#303030'>Link</span></a><span lang=EN-GB
+style='color:black'>]</span></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><a name="OLE_LINK110"><u><span lang=EN-GB
+style='color:black'>All, IGA, IGG, IGM and IGE tabs</span></u></a></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><span lang=EN-GB style='color:black'>In
+these tabs information on the clonal relation of transcripts can be found. To
+calculate clonal relation Change-O is used (Gupta et al, PMID: 26069265).
+Transcripts are considered clonally related if they have maximal three nucleotides
+difference in their CDR3 sequence and the same first V segment (as assigned by
+IMGT). Results are represented in a table format showing the clone size and the
+number of clones or sequences with this clone size. Change-O settings used are
+the </span><span lang=EN-GB>nucleotide hamming distance substitution model with
+a complete distance of maximal three. For clonal assignment the first gene
+segments were used, and the distances were not normalized. In case of
+asymmetric distances, the minimal distance was used.<span style='color:black'> </span></span></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><u><span lang=EN-GB style='color:black'>Overlap
+tab</span></u><span lang=EN-GB style='color:black'> </span></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><span lang=EN-GB style='color:black'>This
+tab gives information on with which (sub)classe(s) each unique analyzed region
+(based on the exact nucleotide sequence of the analyzes region and the CDR3
+nucleotide sequence) is found with. This gives information if the combination
+of the exact same nucleotide sequence of the analyzed region and the CDR3
+sequence can be found in multiple (sub)classes.</span></p>
+
+<p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
+text-align:justify;background:white'><span style='color:black'><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC"> Please note that this tab is based on all
+sequences before filter unique sequences and the remove duplicates based on
+filters are applied. In this table only sequences according more than once are
+included. </span></p>
+
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