Please read the following before posting!
Hi fox, I am doing some analysis on the alpha-diversity on the microbiome data I have. The core-metrics run great but I am having trouble with Chao1. I am using qiime2-2018.11.
I was able to do the rarefaction curve based on Chao1:
qiime diversity alpha-rarefaction
–i-table rarefied_table.qza
–i-phylogeny rooted-tree4.qza
–p-max-depth 25800
–p-metrics chao1
–m-metadata-file samples-info.txt
–o-visualization chao1.qzv
Then I calcualte the Chao1 index:
qiime diversity alpha
–i-table rarefied_table.qza
–p-metric chao1
–o-alpha-diversity Chao1-diversity
This generates a qza file that allows to obtain the tsv file directly (export) or obtaining the qzv file. When I visualize the qzv file I can see the table with the values but there are not box and whiskers, like in the other index of core-metrics.
I can do the box and whiskers in excel with the tsv data, but I am wondering if there is any why to get them represented in qiime2 as for the others in core-metrics.
Thanks
Hi!