Advice on rarefying data

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis

GNU General Public License v3.0

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Advice on rarefying data #611

Closed mradz19 closed 1 year ago

mradz19 commented 1 year ago

I would like to do some alpha diversity analysis on my taxonomic data from my squeezemeta run. Is there any advice on the best way to rarefy the data? From what I have read online alpha diversity should be completed on rarefied data rather than the raw data.

fpusan commented 1 year ago

Hi, You can use vegan to rarefy the data. However to do proper alpha diversity I would rather use marker genes such as 16S rRNA

fpusan commented 1 year ago

Closing due to lack of activity, feel free to reopen