A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi, Eduard. We do not have preset for this protocol. Could you please provide the link of the protocol to us? We can try to help you on setting the parameters to run airrflow. We may also add preset of this protocol in the future.

Hi, thank you for the reply! Here is the link to the kit, with the attached protocol:
<https://www.qiagen.com/gb/products/discovery-and-translational-research/next-generation-sequencing/rna-sequencing/t-cell-receptor-sequencing/qiaseq-targeted-rnaseq-panel-for-t-cell-receptor|https://www.qiagen.com/gb/products/discovery-and-translational-research/next-generat[…]r-sequencing/qiaseq-targeted-rnaseq-panel-for-t-cell-receptor>

Hi everyone, are there any updates on this preset? Alternatively, how can I set up the parameters for this kit? Thank you!

Hi, Andrea <@U0AEHSDJC0H>. We are sorry for the delay. I will have a look of the protocol and try to figure out the parameter setting. I will reach out to you later this week.

Hi, Andrea. I carefully read the protocol introduction provided on the website. I realized that I can't get detailed information needed to set nf-core/airrflow parameters, like the fasta file for primers, location of primer on R1 or R2, location of umi, etc. I am not sure whether this information is available elsewhere. For other protocols where we preset parameters in the pipeline, we usually have not only these technical details but also a small sample dataset that allows us to test and validate the parameter settings.
Do you know where I might be able to obtain sample data generated using this protocol, or documentation that includes these sequencing layout details?

Hi <@U08KDH7QJSV>, thank you for your answer. I also wasn't able to find any official information about read structure. I tried sending a support request to them. In the meantime I was able to find this discussion from the mixcr repo (<https://github.com/milaboratory/mixcr/discussions/1730>). They eventually added support (still in the dev branch) for this kit with this preset but I'm not sure how to convert this to airrflow settings
```
"qiagen-human-rna-tcr-umi-targeted-qiaseq":
  vendor: "QIAGEN"
  label: "QIAseq Targeted RNA Panel Human TCR"
  category: non-generic
  inheritFrom: generic-amplicon-with-umi
  defaultChains:
    - TCRAlpha
    - TCRBeta
    - TCRGamma
    - TCRDelta
  pipeline:
    - align
    - refineTagsAndSort
    - assemble
    - exportClones
  mixins:
    - type: SetSpecies
      species: hsa
    - type: MaterialTypeRNA
    - type: LeftAlignmentBoundaryNoPoint
      floating: false
    - type: RightAlignmentBoundaryNoPoint
      floating: true
      geneType: C
    - type: SetClonotypeAssemblingFeatures
      features: CDR3
    - type: AddQcChecks
      args:
        - type: OverlappedReadsLessBetter
          middle: 0.1
          upper: 0.2
    - type: SetTagPattern
      tagPattern: ^(R1:*) \ ^(UMI:N{14:18})atgcattggagtcct
  align:
    inheritFrom: generic-amplicon-with-umi
    overrides:
      parameters:
        readsLayout: ReverseOnly```

<@U0AEHSDJC0H> The GitHub link you provided contains additional information about the reads. I will need some time to explore it in more detail. By the way, if they provide an analysis tool for assembling the sequences, the assembled data could be used as input for the *assembled mode* in the _nf-core/airrflow_ pipeline.