taxa-bar-plot and rarefying

Dear all,

I have a quick question. I would like to plot some bar graphs to understand the community composition. Is the feature table need to be rarefied prior to plotting taxa bar plot where y axis is relative abundance (%)? As per my understanding, rarefaction is a means of normalization. Once feature table is rarefied, all samples will have the same sampling depth (i.e. 3000 sequences), which means total abundance of each sample will be the same. If I plot taxa bar plot using rarefied data
with abundance (# reads) as y axis, the plot should be exactly same as the one plotted with un-rarefied data with relative abundance (frequency) as y axis, is that right? In this sense, rarefying is equivalent and interchangeable with calculating relative abundance, and once one is done, no need to do the other. Is this correct? Thank you so much.

Best.

Hi @arlandan,

It depends on what you want to use the plot for. My suggestion would be to use unrarified data, since most of our modern feature-based analyses do not assume rarefaction. But, looking at the function in QIIME, you could pass either.

Best,
Justine

Hi @jwdebelius,
Thank you for your reply. Would you be able to give some comments on my second question as well?

Thank you very much. I really appreciate your help.

Best.

Hi @arlandan,

We have a discussion about normalisation about every 2 weeks to a month around here, and a lot end up just referencing previous posts. This isn’t to discourage you from asking questions, particularly if you can’t find something that specifically speaks to your issue, but Id recommend a quick search of the forum because lots of people have already talked about it.

Best,
Justine

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