annotate complete_immunerepertoire.xml @ 53:0ef7f80ea061 draft

Uploaded
author davidvanzessen
date Thu, 25 Feb 2021 13:39:50 +0000
parents 124b7fd92a3e
children 81b3eb11ed2c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
52
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
1 <tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.0">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
2 <requirements>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
3 <requirement type="package" version="2.3">r-gridextra</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
4 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
5 <requirement type="package" version="1.8.4">r-plyr</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
6 <requirement type="package" version="1.11.4">r-data.table</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
7 <requirement type="package" version="1.4.3">r-reshape2</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
8 <requirement type="package" version="1.3.0">r-lymphclon</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
9 <requirement type="package" version="1.2.4">r-stringi</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
10 <requirement type="package" version="1.3.1">r-stringr</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
11 <requirement type="package" version="0.69.6">circos</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
12 <requirement type="package" version="0.23">circos-tools</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
13 </requirements>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
14 <description> </description>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
15 <command interpreter="bash">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
16 complete.sh "
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
17 #for $i, $f in enumerate($patients)
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
18 "${f.id}"
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
19 #for $j, $g in enumerate($f.samples)
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
20 ${g.sample}
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
21 #end for
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
22 #end for
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
23 " $out_file $out_file.files_path "$clonaltype"
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
24 #if $gene_selection.source == "imgtdb"
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
25 "${gene_selection.species}" "${gene_selection.locus}" $filterproductive ${clonality_method}
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
26 #else
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
27 "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
28 #end if
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
29 </command>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
30 <inputs>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
31 <repeat name="patients" title="Donor" min="1" default="1">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
32 <repeat name="samples" title="Replicate" min="1" default="1">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
33 <param name="sample" type="data" label="Replicate to Process" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
34 </repeat>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
35 <param name="id" type="text" label="ID" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
36 </repeat>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
37 <param name="clonaltype" type="select" label="Clonal Type Definition">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
38 <option value="none">Don't remove duplicates based on clonaltype</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
39 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3 (AA)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
40 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3 (nt)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
41 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3 (AA)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
42 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3 (nt)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
43 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3 (nt)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
44 </param>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
45
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
46 <conditional name="gene_selection" >
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
47 <param name="source" type="select" label="Order of V(D)J genes in graphs" help="" >
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
48 <option value="imgtdb" selected="true">IMGT-DB</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
49 <option value="custom">User defined</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
50 </param>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
51 <when value="imgtdb">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
52 <param name="species" type="select" label="Species">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
53 <option value="Homo sapiens functional">Homo sapiens functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
54 <option value="Homo sapiens">Homo sapiens</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
55 <option value="Homo sapiens non-functional">Homo sapiens non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
56 <option value="Bos taurus">Bos taurus</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
57 <option value="Bos taurus functional">Bos taurus functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
58 <option value="Bos taurus non-functional">Bos taurus non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
59 <option value="Camelus dromedarius">Camelus dromedarius</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
60 <option value="Camelus dromedarius functional">Camelus dromedarius functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
61 <option value="Camelus dromedarius non-functional">Camelus dromedarius non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
62 <option value="Canis lupus familiaris">Canis lupus familiaris</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
63 <option value="Canis lupus familiaris functional">Canis lupus familiaris functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
64 <option value="Canis lupus familiaris non-functional">Canis lupus familiaris non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
65 <option value="Danio rerio">Danio rerio</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
66 <option value="Danio rerio functional">Danio rerio functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
67 <option value="Danio rerio non-functional">Danio rerio non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
68 <option value="Macaca mulatta">Macaca mulatta</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
69 <option value="Macaca mulatta functional">Macaca mulatta functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
70 <option value="Macaca mulatta non-functional">Macaca mulatta non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
71 <option value="Mus musculus">Mus musculus</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
72 <option value="Mus musculus functional">Mus musculus functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
73 <option value="Mus musculus non-functional">Mus musculus non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
74 <option value="Mus spretus">Mus spretus</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
75 <option value="Mus spretus functional">Mus spretus functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
76 <option value="Mus spretus non-functional">Mus spretus non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
77 <option value="Oncorhynchus mykiss">Oncorhynchus mykiss</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
78 <option value="Oncorhynchus mykiss functional">Oncorhynchus mykiss functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
79 <option value="Oncorhynchus mykiss non-functional">Oncorhynchus mykiss non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
80 <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
81 <option value="Ornithorhynchus anatinus functional">Ornithorhynchus anatinus functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
82 <option value="Ornithorhynchus anatinus non-functional">Ornithorhynchus anatinus non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
83 <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
84 <option value="Oryctolagus cuniculus functional">Oryctolagus cuniculus functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
85 <option value="Oryctolagus cuniculus non-functional">Oryctolagus cuniculus non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
86 <option value="Rattus norvegicus">Rattus norvegicus</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
87 <option value="Rattus norvegicus functional">Rattus norvegicus functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
88 <option value="Rattus norvegicus non-functional">Rattus norvegicus non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
89 <option value="Sus scrofa">Sus scrofa</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
90 <option value="Sus scrofa functional">Sus scrofa functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
91 <option value="Sus scrofa non-functional">Sus scrofa non-functional</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
92 </param>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
93
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
94 <param name="locus" type="select" label="Locus">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
95 <option value="TRA">TRA</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
96 <option value="TRD">TRD</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
97 <option value="TRG">TRG</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
98 <option value="TRB">TRB</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
99 <option value="IGH">IGH</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
100 <option value="IGI">IGI</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
101 <option value="IGK">IGK</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
102 <option value="IGL">IGL</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
103 </param>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
104 </when>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
105 <when value="custom">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
106 <param name="species" type="hidden" value="custom" size="50" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
107 <param name="vgenes" type="text" label="V Genes, add the custom genes comma seperated, no spaces" size="100" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
108 <param name="dgenes" type="text" label="D Genes" size="100" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
109 <param name="jgenes" type="text" label="J Genes" size="100" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
110 </when>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
111 </conditional>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
112
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
113 <param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs ">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
114 <option value="yes">Yes</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
115 <option value="no">No</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
116 </param>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
117
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
118 <param name="clonality_method" type="select" label="Shared clonal types / clonality">
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
119 <option value="none">Do not determine overlap (only 1 replicate present)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
120 <option value="old">Determine the number of sequences that share the same clonal type between the replicates</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
121 <option value="boyd">Determine the clonality of the donor (minimal 3 replicates)</option>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
122 </param>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
123 </inputs>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
124 <outputs>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
125 <data format="html" name="out_file" />
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
126 </outputs>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
127 <requirements>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
128 <requirement type="package" version="0.6">igblastwrp</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
129 <requirement type="package" version="3.3">weblogo</requirement>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
130 <!--<requirement type="package" version="0.20">circostools</requirement>-->
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
131 </requirements>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
132 <help>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
133 <![CDATA[
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
134 **References**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
135
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
136 Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ (2009). Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. In *Science Translational Medicine 1(12):12ra23*.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
137
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
138 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
139
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
140 **Input files**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
141
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
142 IMGT/HighV-QUEST .zip and .txz files and FASTA files are accepted as input files. In addition filtered IMGT files generated using the SHM &amp; CSR pipeline can be used as input files.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
143 Note: Files can be uploaded by using “get data” and “upload file”. When uploading IMGT files “IMGT archive“ should be selected as a file type. When uploading FASTA files the auto-detect function can be used to select a file type. Special characters should be prevented in the file names of the uploaded replicates as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
144
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
145 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
146
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
147 **Donor and replicates**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
148
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
149 The immune repertoire pipeline can analyse files from multiple donors in parallel. Therefore for each analysed donor an ID has to be given. This ID can only contain letters, numbers and _. Spaces in the ID give an error when running the immune repertoire pipeline. In the default setting of the immune repertoire pipeline one donor consisting out of one replicate can be uploaded. However, multiple replicates per donor can be uploaded by using the "Add new replicate" button. In addition, multiple donors van be added by using the insert donor button. The multiple replicate option can be used when multiple data files from the same donor are available. For the calculation of the clonality score using the algorithm described by Boyd et al (PMID: 20161664) at least 3 replicates have to be included per donor.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
150
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
151 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
152
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
153 **Clonal Type Definition**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
154
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
155 Allows the selection of a single sequence per clone. Different definitions of a clone can be chosen.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
156
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
157 .. class:: infomark
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
158
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
159 Note: The first sequence (in the data set) of each clone is always included in the analysis. This means that altering the data order (by for instance sorting) can change the sequence which is included in the analysis and therefore slightly influence results.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
160
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
161 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
162
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
163 **Order of V(D)J genes in graphs**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
164
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
165 This setting allows you to order the V(D)J genes in the graphs in a user defined order. When using the default “IMGT-DB” all genes in the V, D an J gene graphs will be ordered based on their IMGT numbering. By selecting user defined the order of the V, D and J genes in the graphs can be altered according to the users personal settings. For simplifying of visualizing the genes in the chromosomal order the order of V, D and J genes on the chromosome in are included at the bottom of this help page. For any other ordering please provide the order of gene names divided by commas.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
166
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
167 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
168
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
169 **Species**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
170
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
171 Enter the species of the replicates(s) you would like to analyse.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
172
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
173 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
174
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
175 **Locus**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
176
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
177 A dropdown menu to select the immune receptor locus to be analysed.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
178
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
179 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
180
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
181 **Remove unproductive sequences from graphs**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
182
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
183 This filter provides the option to only include productive sequences or both productive and unproductive sequences in the graphs.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
184
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
185 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
186
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
187 **Shared clonal types / clonality**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
188
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
189 This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a replicate no sequences overlap or clonality can be determined and therefore the “do not determine overlap” option should be selection. The “Determine the number of sequences that share the same clonal type between the replicates” option allows the user to determine the number of overlapping sequences (based on the clonal type definition defined in the ‘clonal type definition filter’) between different replicates. This can be used to for instance look at different time point in the same donor to changes in the repertoire. When three or more replicates of the same blood same are amplified and sequences in parallel, the “determine clonality of the donor” function can be used to calculate the number of overlapping sequences as well as the clonality score as described by Boyd et al, PMID: 20161664.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
190
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
191 -----
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
192
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
193 **Execute**
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
194
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
195 Upon pressing the execute button a new analysis is added to your history (right side of the page). Initially this analysis will be grey, after initiating the analysis colour of the analysis in the history will change to yellow. When the analysis is finished it will turn green in the history. Now the analysis can be opened by clicking on the eye icon on the analysis of interest. When an analysis turns red an error has occurred when running the analysis. If you click on the analysis title additional information can be found on the analysis. In addition a bug icon appears. Here more information on the error can be found.
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
196 ]]>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
197 </help>
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
198
124b7fd92a3e Uploaded
davidvanzessen
parents: 50
diff changeset
199 </tool>