# Rarefy metagenome sequence data before MetaPhlAn3 analysis

**URL:** <https://forum.biobakery.org/t/rarefy-metagenome-sequence-data-before-metaphlan3-analysis/690>\
**Category:** MetaPhlAn\
**Created:** [July 9, 2020, 1:19pm UTC](https://forum.biobakery.org/t/rarefy-metagenome-sequence-data-before-metaphlan3-analysis/690 "2020-07-09T13:19:08Z")\
**Posts on this page:** 1\
**Showing post:** 4

<div class="post-metadata">

**Author:** ![paolinomanghi](https://avatars.discourse-cdn.com/v4/letter/p/839c29/32.png) [@paolinomanghi](https://forum.biobakery.org/u/paolinomanghi)\
**Post date:** [July 10, 2020, 10:23am UTC](https://forum.biobakery.org/t/rarefy-metagenome-sequence-data-before-metaphlan3-analysis/690/4 "2020-07-10T10:23:56Z")

</div>

Hi @DEEPCHANDA7 , a common rarefaction procedure is to rarefy each sample to the 10th percentile of the dataset, meaning that 10% of the sample will be below the threshold and will be excluded.

You can subset to the 10% percentile either the raw-reads or the bowtie alignment (and passing the rarefied bowties as input to metaphlan). I can’t think of any procedure capable of rarefying directly the taxonomic profiles.

Since doing rarefaction you will not loose 10% of the samples (in case you apply this type of rarefaction) but you will also loose great part of the sample diversity, I would personally use the rarefacted profiles just for alpha-diversity. Since 2.2 GB is a normal size and 600 MB is a medium-small size for a metagenome, in your case I would personally go with rarefaction, but just for the alpha-diversity computation.

Thanks,  
Paolo

---

_[View the full topic](https://forum.biobakery.org/t/rarefy-metagenome-sequence-data-before-metaphlan3-analysis/690)._