Hi, I am new to the package. I noticed that "define_clones" folder results of clonal_diversity.tsv files from all_reps_clone_report folder (containing all samples) and an individual sample report folder are different ,such as "d" diversity score with q=0 as an example. Are there any transformation done on "d" from individual sample to be included in all_reps_clone_report? Which 'd' score, should a user to choose ? Thanks so much for any suggestion!

Hi Jin, could you share an example of this happening? I think it is due to the bootstrapping sample used in each case to compute diversity, as it is taken as the number of sequences in the sample with least sequences, so when considering all repertoires together, this number will be different.

I noticed it even in airrflow demo example here

Yes this is due to the boostrapping sample: when computing diversity, all samples used for diversity computation are bootsrapped without replacement to the number of sequences of the sample with the fewest amount of sequences. So if one sample has less sequences than another, when including them together for the diversity calculation the results can differ.

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We use the Hill Diversity index for diversity calculation