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metagenlab / zAMP

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
https://zamp.readthedocs.io/en/latest/
MIT License
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Sample with less reads than the rarefaction cut-off are dropped #8

Closed valscherz closed 5 years ago

valscherz commented 5 years ago

Using phyloseq rarefaction function, the samples containing less reads than the cut-off are dropped.

valscherz commented 5 years ago

Corrected by commit 2febfdcf3b173289fbdc3ad1dda265eab7fb397d, using vegan rrarefy instead of phyloseq.

valscherz commented 5 years ago

Changes made in 2febfdcf3b173289fbdc3ad1dda265eab7fb397d did not work properly; the rarefaction was done based on the sum of each taxa instead of each sample. This is due to the fact that vegan needs OTUs in colums and samples in rows. This is corrected by commit 80878a051cedca7725f7effcae9356678cfa3071