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phbradley / tcr-dist

Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
MIT License
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Track the clonality of out of frame CDR3s #19

Open jeremycfd opened 6 years ago

jeremycfd commented 6 years ago

I think currently we exclude all out of frame CDR3s from any part of the analysis after sequence parsing. It's good to exclude these from analysis since they are non-functional, but it is important to track their clonality, as they are a correlate of clonality signals for functional CDR3s.

phbradley commented 6 years ago

Would we want their clonality to contribute to estimates of clonality for their parent repertoires, or should it be reported separately? And when you say clonality, you mean the overall distribution of clone sizes, or the actual clone sizes for all the out-of-frames?

jeremycfd commented 6 years ago

To clarify, I think we need to report the clonal size of out-of-frame CDR3s somewhere; it shouldn't impact the clonality estimates for in-frame CDR3s.