Alpha rarefaction question: sequencing depth vs "frequency"

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1

Hi all,

According to the Moving Picture Tutorial steps, the “feature-table summarize” tool generates a table.qzv. From this file, they use the interactive sample detail tab to pick where to rarefy the data, 1103 for the tutorial, which is labeled “Frequency.” At first, I thought this was frequency of features, but is this actually the number of sequences present in each sample?

The “frequency” numbers in the example table.qzv line up pretty exactly with the end point of the curves in the alpha-rarefaction.qzv that they plot later, and in this plot x-axis is labeled sequencing depth. The same holds for my data.

I just want to be very sure, as we talk about frequency of features so much, that seeing “frequency” here to mean “number of sequences,” was confusing me.

Thanks in advance for the clarification!

2

That's right! Frequencies means counts in this example.

The feature-table summarize command will give you information on how many sequences are associated with each sample and with each feature, histograms of those distributions, and some related summary statistics.

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