What metrics to use to calculate variant library evenness or uniformity or bias
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8 months ago
eli_bayat ▴ 90

I have a 15k library of variants (OTUs) from a genome region. I want to compare the evenness of this library and understand of the library bias.

I tried different methods to calculate evenness or uniformity of this library such as Shannon evenness index, relative abundance rank plot, kurtosis , skewness. I am confused with the results and why they are not aligned. For example my Shannon evenness index is 0.98 which means library is very even, while my kurtosis is very large (120), indication not uniform distribution.

I should note that for calculating kurtosis I use relative abundance which is read count of every variant /total read count of all variants in that library.

My question is what metrics I can use to have a better understanding of library evenness or uniformity, other that above metrics, and why my results are so contradictory?


library-bias variant • 334 views

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