mixcr/src/main/resources/presets/protocols/idt.yaml at develop · milaboratory/mixcr · GitHub

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idt-human-rna-tcr-umi-archer:
  vendor: "Integrated DNA Technologies"
  label: "Archer IMMUNOVerse TCR panel"
  category: non-generic
  inheritFrom: generic-amplicon-with-umi
  defaultChains:
    - TCRAlpha
    - TCRBeta
  pipeline:
    - align
    - refineTagsAndSort
    - assemble
    - exportClones
  mixins:
    - type: SetSpecies
      species: hsa
    - type: MaterialTypeRNA
    - type: SetTagPattern
      tagPattern: ^(UMI:N{8})N{13}(R1:*)\^(R2:*)
    - type: LeftAlignmentBoundaryNoPoint
      floating: false
    - type: RightAlignmentBoundaryNoPoint
      floating: true
      geneType: C


idt-human-rna-bcr-umi-archer:
  vendor: "Integrated DNA Technologies"
  label: "Archer IMMUNOVerse BCR panel"
  category: non-generic
  inheritFrom: idt-human-rna-tcr-umi-archer
  defaultChains:
    - IGHeavy
    - IGLight
  pipeline:
    - align
    - refineTagsAndSort
    - assemble
    - exportClones
  mixins:
    - type: SetSplitClonesBy
      geneType: C
      value: true
    - type: AddExportClonesField
      field: -isotype
      insertIndex: -1
      args:
        - auto
    - type: SetClonotypeAssemblingFeatures
      features: [ "VDJRegion" ]