Hi, we use --p-max-depth in alpha rarefaction curve and --p-sampling-depth at alpha diversity analysis step. Are these both same or there is a difference? Thanks

The min and max depths are effectively the range of the x axis on the alpha rare plot. You cannot rarefy lower than 0, so that handles the min depth. For the max, you can only rarefy to as many features are present in your most populated sample. For example, from the Moving Pictures tutorial : [ima…

Hi @Yogesh_Gupta , The p--min-depth parameter on the alpha rarefaction curve is the smallest depth where you want to rarify your data. This should be lower than whatever your smallest sampling depth is, probably. The rarefaction curve varies your sampling depth to calculate diversity, and can help y…

Hi @jwdebelius , Thanks, I am using qiime2,2018.11 and following the moving tutorial in which alpha diversity step comes first and then alpha rarefaction. are you suggesting both value should be same, that we decide based on qiime feature-table summarize output to choose the maximum value while re…

[image] Yogesh_Gupta: which alpha diversity step comes first and then alpha rarefaction. That is just how that tutorial presents it. You can also run alpha rare before core metrics phylo, and use the results from alpha rare to make a decision about what even sampling depth to use. [image] …

Thanks. I understand how to decide value for --p-sampling-depth in core-metrics-phylogenetic analysis, it is based on feature-table summarize. But still confused on how to decide value for --p-max-depth alpha-rarefaction? It will be great help if you can help me to understand it. Thanks again!

sorry for posting on other question, I removed from question from that topic: Hi @thermokarst , here is details of samping depth for my data: here is the depth summary of sample: > summary(depths) Min. 1st Qu. Median Mean 3rd Qu. Max. 18396 77714 103546 112311 135904 308487 so In core-metric…

[image] Yogesh_Gupta: is it ok? Your alpha rarefaction is fine - it doesn't matter what value you use there --- the only impact is the extent of the x-axis in the resulting plot. For the core-metrics-phylo command, I can't really answer that --- even sampling depth is a bit subjective, and i…

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Confused about --p-sampling depth and and --p-max-depth

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