Postanalysis

[Januaryyiyue]

Hello,

While running mixcr postanalysis, I calculated TCR diversity and got something like this:

sample	Observed diversity	Shannon-Wiener diversity	Normalized Shannon-Wiener index	Inverse Simpson index	Gini index	Chao1 estimate	Efron-Thisted estimate	d50
Sample1_mixcr_out.clns	857.0	666.640136403944	0.9628059742404645	532.7401162816606	1.0018770878509762	857.0	996.0	208.0
Sample2_mixcr_out.clns	0.0	1.0	-0.0	-Infinity	1.0	0.0	0.0	0.0

I checked Sample2 and there are more than 100 clones. I was wondering what I can do to fix this. Thank you!

[mizraelson]

I think you used --drop-outliers, and the smaller sample was dropped. Keep in mind that diversity metrics don’t really make much sense for samples with a very low number of clones, such as 100.