Skip to content

Latest commit

 

History

History
18 lines (11 loc) · 2.71 KB

README.md

File metadata and controls

18 lines (11 loc) · 2.71 KB
Raw

data/analysis-individual/

This repository contains data generated when you preprocess raw fastq files into ASV and taxonomic tables. Our meta-analysis included 13 datasets, so there are 13 sub-directories (+ CLUSTER sub-directory). Even though we used a standardized pipeline to preprocess the data for all datasets, we still have separate directories & scripts as there are subtle differences between datasets (e.g. cleaning up metadata tables, different primer sequences, ...). However, we structured all these sub-directories in a similar way.

Structure of each dataset sub-directory

Within each sub-directory, you will find:

  1. A 01_Dada2-NameDataset/ folder, in which you will save .rds files as checkpoints when running the 01_Dada2-NameDataset.Rmd script (in the corresponding scripts sub-directory);
  2. A filtered1/ and filtered2/ folders, in which .fastq files will be generated during primer removal and quality-filtering of the reads (respectively), again using the 01_Dada2-NameDataset.Rmd script (in the corresponding scripts sub-directory);
  3. A 03_EDA-NameDataset/ folder, in which you will save normalized phyloseq objects as .rds files, and also save plots when running the 03_EDA-NameDataset.Rmd script (in the corresponding scripts sub-directory).

CLUSTER sub-directory

This subdirectory is made to store data & scripts to run on your lab's computer clusters (server/high-performance computing). There are two tasks that we recommend running on a cluster:

  1. Assigning taxonomy: after inferring ASVs, we align their sequence to the Silva database. You can copy the CLUSTER/taxonomy/ folder to your cluster & submit a job with the bash_assignTaxonomy.sh script, it will assign taxonomy for all ASV tables present in the CLUSTER/taxonomy/input/ subfolder. Taxonomic tables will be saved as an .rds object in the CLUSTER/taxonomy/output/ subfolder, so you can copy only the output/ subfolder back to your computer.
  2. Phylogenetic trees: to infer a phylogenetic tree and add it to your phyloseq object, you can copy the CLUSTER/phylotree/ folder to your cluster & submit a job with the bash_phylotree_cluster.sh script. It will compute a phylogenetic tree for all phyloseq objects present in the CLUSTER/phylotree/input/ subfolder. Phyloseq objects containing a phylogenetic tree will be saved as an .rds object in the CLUSTER/phylotree/output/ subfolder, so you can copy only the output/ subfolder back to your computer.