MaAslin

Description

Maaslin is a multivariate analysis tool.

Install Tools

Download QIIME-to-Maaslin to your HOME folder.

# Download qiimetomaaslin to your HOME folder
wget -P ~/ https://bitbucket.org/biobakery/qiimetomaaslin/downloads/qiimetomaaslin.zip

# Decompress the package
unzip ~/qiimetomaaslin.zip

Download Maaslin to your HOME folder.

# Download MaAslin to your HOME folder
wget -P ~/ https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.4.tar.gz

# Decompress the package
tar -xvf ~/Maaslin_0.0.4.tar.gz

Install other dependencies

# install required python packages
pip install blist
pip install biopython

# Install the package and dependencies
R CMD INSTALL  ~/Maaslin_0.0.4.tar.gz

Usage

Convert BIOM file to text format

TODO TEXT

# Convert OTU table to txt
biom convert \
-i otu_table.biom \
-o otu_table.tsv \
--to-tsv \
--header-key taxonomy

Creating a mapping file

TODO TEXT. If you are editing the mapping file in Excel, it is crucial that you save the table as a Windows-Formatted .txt file when are you finished editing the columns of interest. If this step is skipped, you may have errors when running the next main command.

Merge metadata and OTU abundance counts

TODO TEXT

python ~/qiimetomaaslin/src/qiimeToMaaslin.py \
otu_mapping_filtered.txt < otu_table.tsv > maaslin_input.pcl

Run MaAslin

TODO TEXT

Rscript ~/Maaslin_0.0.3/R/Maaslin.R \
--lastMetadata 13 \
--fdr 0.05 \
maaslin_input.pcl \
maaslin_output