odd alpha rarefaction curve

Hi all, it's my first time to see this type of odd alpha-rarefaction curve. It usually from 0 and up to plateau. Is anyone willing to share with me what is this means and why it happens, please? Thank you.

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Hello Alex,

Wow, that is a supprising graph!

How many samples did you include here?
What do the other rarefaction graphs look like (I'm especially interested in observed features)?

Hi @colinbrislawn, the other graphs look similar to this, up and down, and I noticed that the non-chimeric is all zero (except one of the samples 0.4). Is this due to a primer issue? And my concern is whether this data set is still valid? Thanks for your help in advance!

@colinbrislawn 24 samples, 4 groups. Any reason why it looks like this? I can't explain what is this means.

That sounds reasonable. Having >50k reads per sample is also extremely reasonable, so I'm wondering if something else is going on...

Can you rerun this analysis showing 5k to 50k reads per sample? By looking at the sample loss in the graph below 50k reads per sample, we will be seeing results from all 24 of your samples.

Can you also post the command you ran?


It is interesting that the plot is back to normal (starting from 0 up to plateau, and around 30,000 non-chimeric reads) after I re-run the analysis. I am not sure what's happening, but will posted here if the same issue happen again

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I'm glad it's working for you.

Alex, can you please post the plot and command to help future users with the same question?

I suspect that after 50k, samples without that many reads are being dropped causing the graph to jump around. We can confirm that once you post the plot.


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