Mercurial > repos > davidvanzessen > argalaxy_tools

comparison complete_immunerepertoire.xml @ 19:3ef457aa5df6 draft

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author davidvanzessen
date Thu, 22 Dec 2016 03:43:02 -0500
parents 5d11c9139a55
children 4d2a8f98a502
comparison
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18:5d11c9139a55 19:3ef457aa5df6
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128 **Input files** 128 **Input files**
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130 IMGT/HighV-QUEST .zip and .txz files and FASTA files are accepted as input files. In addition filtered IMGT files generated using the SHM & CSR pipeline can be used as input files. 130 IMGT/HighV-QUEST .zip and .txz files and FASTA files are accepted as input files. In addition filtered IMGT files generated using the SHM & CSR pipeline can be used as input files.
131 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 samples as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names. 131 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.
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135 **Donor and replicates** 135 **Donor and replicates**
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137 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 sample can be uploaded. However, multiple samples per donor can be uploaded by using the insert sample button. In addition, multiple donors van be added by using the insert donor button. The multiple sample 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 samples have to be included per donor. 137 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.
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141 **Clonal Type Definition** 141 **Clonal Type Definition**
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157 **Species** 157 **Species**
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159 Enter the species of the sample you would like to analyse. 159 Enter the species of the replicates(s) you would like to analyse.
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163 **Locus** 163 **Locus**
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175 **Shared clonal types / clonality** 175 **Shared clonal types / clonality**
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177 This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a sample 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. 177 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.
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181 **Execute** 181 **Execute**
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