I have a naive question about whether all VDJs have equal chance to be detected.
How do you know whether there is any bias in covering the theoretical VDJ repertoire, and if so, how much can be explained by the nature of the wetlab technique (e.g. chromium VDJ primers, or BIOMED2 primers choosing a restricted set of VJ primers), versus downstream challenges (the assembly algorithm, genomic loci similarity unresolved by short reads). I'm not sure what the proper gold standard here would be: high depth bulk RNAseq on enriched Tcells? tabulations of counts across all theoretical VJ pairings according to IMGT?
Hello,
I have a naive question about whether all VDJs have equal chance to be detected.
How do you know whether there is any bias in covering the theoretical VDJ repertoire, and if so, how much can be explained by the nature of the wetlab technique (e.g. chromium VDJ primers, or BIOMED2 primers choosing a restricted set of VJ primers), versus downstream challenges (the assembly algorithm, genomic loci similarity unresolved by short reads). I'm not sure what the proper gold standard here would be: high depth bulk RNAseq on enriched Tcells? tabulations of counts across all theoretical VJ pairings according to IMGT?
EDIT: I should add that on reading through the tracer paper and supplementary notes, I still had this question.
Thanks!