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Pseudobulking 10x scRNA TCR sequencing #33

@dltamayo

Description

@dltamayo

Pseudobulking by collapsing individual cell TCRs will enable outputs from scRNA TCR sequencing to be used as inputs for TCRtoolkit-bulk.

Initial implementation:

  • for consistency, align scRNA TCR modality fastqs using the SCRATCH pipeline
  • take airr_rearrangement.tsv as input for pseudobulk module
  • group by full nucleotide (at least initially, or by some other metric)
  • retrieve clonal counts per full nucleotide
  • extract or infer necessary columns for any further standardization (see Standardizing inputs to AIRR format #32)
  • test that standardized pseudobulk output is compatible for downstream processes

Grouping by full nucleotide will be the closest simulation of bulk TCR sequencing.

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