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Old 01-05-2010, 01:36 PM   #1
psong
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Location: Boston

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Wink step by step for rarefaction calculation

I am very new to this. Can anyone explain to me how to calculate the rarefaction based on COG category counts? And how to calculate species richness based on the 16s sequence. What are the minimum data requirement?

Many thanks!!
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Old 01-06-2010, 05:08 AM   #2
psong
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I found two websites that will calculate rarefaction for you:
http://biome.sdsu.edu/fastgroup/cal_tools.htm
and
http://pyro.cme.msu.edu/spring/rarefaction.spr
It seems that you'll first need to align your sequences, then cluster them. Finally you submit the cluster file for rarefaction calculation.

Anyone care to explain more about how to interpret data and draw graphs using the output files?
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