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2 / 22 of 2 issues completedDescription
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.tsvas 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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