Module 5: 16S analysis pipeline - important links - Githubissues

wanjauk / intbt_2020

Training material for H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics Training 2020

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Module 5: 16S analysis pipeline - important links #1

Open wanjauk opened 4 years ago

wanjauk commented 4 years ago

Important links:

Tutorial site: https://iallali.github.io/DADA2_pipeline/16SrRNA_DADA2_pipeline.html
Script used in the tutorial: https://raw.githubusercontent.com/mbbu/intbt_2019/master/Module_5_16S_analysis_pipeline/dada2_pipeline_tutorial.R
Required tutorial data: http://web.cbio.uct.ac.za/~gerrit/downloads/dog_stool_full.tgz
RefSeq-RDP 16S database: https://zenodo.org/record/3266798/files/RefSeq-RDP16S_v3_May2018.fa.gz

Create an R project called dada2_tutorial_dog and then download the script, tutorial data and database by copying and pasting the following on the linux terminal (on the HPC's RStudio):

Script wget https://raw.githubusercontent.com/mbbu/intbt_2019/master/Module_5_16S_analysis_pipeline/dada2_pipeline_tutorial.R
Tutorial data wget http://web.cbio.uct.ac.za/~gerrit/downloads/dog_stool_full.tgz Note: unzip the data using the following: mkdir -p dog_samples && tar -xvzf dog_stool_full.tgz -C dog_samples
RefSeq-RDP database wget https://zenodo.org/record/3266798/files/RefSeq-RDP16S_v3_May2018.fa.gz