##Introduction This is a repository to help recreate the microbiota analysis from the mansucript “Obesity-Dependent Increases in Oocyte-Specific mRNAs are associated with Increases in Pro-Inflammatory Signaling and Gut Microbial Abundance of Lachnospiraceae.”

##To recreate the microbiota analysis:

The script below to recreate the analysis will download and install all software dependencies using Anaconda and subsequently complete the analysis. The final output is a file to upload to MaAsLin on Galaxy to identify correlations between OTUs and associated metadata.

Due to licensing issues, USEARCH could not be included as a dependency that is automatically downloaded and installed. To obtain a download link, go to the USEARCH download page and select version USEARCH v7.0.1090 for mac. A link (expires after 30 days) will be sent to the provided email. Use the link as an argument for shell script below.

To begin, simply clone this repository and run the recreate_analysis.sh script (provide the link to download your licensed USEARCH version as an argument for setup.sh):

• git clone https://github.com/chrisLanderson/2016_Xie_et_al.git
• cd 2016_Xie_et_al
• ./recreate_analysis.sh usearch_link

Anaconda is downloaded first and prompts you during installataion of the dependencies for the analysis, such as QIIME. The prompts are as follows:

• Press enter to view the license agreement
• Press enter to read the license and q to exit
• Accept the terms
• Prompts you where to install anaconda. Simply type anaconda to create a directory within the current directory. Should be: [/Users/user/anaconda] >>> anaconda
• No to prepend anaconda to your path. Choosing yes should not impact the installation though.
• Will be asked a few times if you wish to proceed with installing the packages…agree to it.

After installation the analysis will begin and eventually generate an output (wood.otu_table.upload_maaslin.txt) to be used as an input for MaAsLin on Galaxy to identify correlations between OTUs and metadata.