Hello Megan community,
Does anyone have tips or links to helpful step-by-step on for making taxonomy rarefaction curves in MEGAN6? I tried making one with 6 different datasets but the result doesn’t look very curvy. It seems it only samples the maximum number of leaves and plots one data point when I try to export the results.
Thank you.
Could you maybe provide a picture with this problem, so it is easier to estimate what went wrong?
This is an example of a rarefaction plot made with MEGAN 6.4.20 Ultimate Version of 20 samples.
test.pdf (18.2 KB)
Hello Sina,
Thanks for the reply. I’ve attached an example of what I get when I try to make a rarefaction curve. phyla.pdf (29.7 KB)
Your datasets in this case are much bigger. Look at the different scaling of the x axis. My example would look similar if scaled this way.
Your samples are fine, they are just “over sequenced”. You would have needed only about 25000 reads to capture the taxonomic diversity found in the data. Of course this is not a bad thing, as you can now have better functional and quantitative analysis.
Is it possible to maximize the X axis to 25000?
The max-value of the x-axis is set to match the number of reads. Let me check that I understand your question: Are you requesting a feature that allows the user to set the x-axis max-value to something different?
Yes I wanted to set the max val if possible