Module 6: 16S downstream analyses in R

[wanjauk]

Session 1

Important links:

• Module website: https://kviljoen.github.io/H3ABioNet_16S/
• DADA2 nextflow pipeline: https://github.com/grbot/16S-rDNA-dada2-pipeline
• Instructions on running Nextflow DADA2 pipeline: https://github.com/mbbu/Tutorials-software-guide/blob/master/Tutorials/Dada2%20Pipeline/Running%20the%20DADA2%20Nextflow%20pipeline%20on%20test%20data.md
• Nextflow output: https://github.com/wanjauk/intbt_2020/blob/master/Downstream_Analysis_in_R/Session_1_Nextflow_demo/nextflow-demo-out.zip

[wanjauk]

Session 2

1. Go to https://hpc01.icipe.org/rstudio/auth-sign-in and login with your username and password.
2. Create a new project in RStudio called R_downstream
3. Download the required files for this session by copying and pasting the commands below on the Linux terminal on icipe's RStudio:

• wget https://raw.githubusercontent.com/wanjauk/intbt_2020/master/git-download.sh
• bash git-download.sh https://api.github.com/repos/wanjauk/intbt_2020/contents/Downstream_Analysis_in_R && mv Session_2_Importing_data/* . && rmdir Session_2_Importing_data && unzip Session_1_Nextflow_demo/nextflow-demo-out.zip && rm -rf Session_1_Nextflow_demo