Alpha rarefaction plotting and sampling (i.e. rarefaction) depth are difficult to understand?

[khaknasheen]

Dear Sir,

I have read the sampling depth and alpha rarefaction plotting from the moving picture tutorials. Both have confused me. For diversity analysis, we apply --p-sampling-depth, which randomly subsample the counts from each sample. We are looking at the sequence count in table.qzv. If sequence counts in certain samples is less than 1000, we do not pass them to diversity analysis. After diversity analysis in moving pictures tutorials, a small portion is about the rarefaction plotting, where --p-max-depth is put from the frequency per sample in the Table.qzv particularly near to median frequency. We got two plots alpha rarefaction plots and bottom plots. I am very much confused between the sampling depth and alpha rarefaction plottings. The question is where we have to put the sampling depth and alpha rarefaction plotting when doing analysis and what is the importance. Is there any difference between them? I have seen several rarefied curves in the literature. Why we rarefied after diversity analysis? What is Waiting for a positive response.

Thanks

[Nicholas_Bokulich]

Hi @khaknasheen,
This is a duplicate of this question:

Can someone help in Alpha rarefaction plotting depths?

Dear All, In the section Alpha rarefaction plotting, I could not understand the min and max depth. Here in the following parameters of moving pictures tutorial the p-max-depth kept at 4000. Qiime diversity alpha-rarefaction –i-table table.qza –i-phylogeny rooted-tree.qza *–p-max-depth 4000 * –m-metadata-file sample-metadata.tsv –o-visualization alpha-rarefaction.qzv For my sample what value I choose? from where this value comes from? What is the importance of this rarefaction plottin…

Please read that post and the tutorials and forum links attached there to answer your questions.