Aeration and mineral composition of soil determine microbial CUE and OM retention
Analysis of stable-isotope probing experiment included in the paper: [Aeration and mineral composition of soil determine microbial CUE and OM retention]
Overview
├── DADA2_pseudo # ASV table, taxonomy phylogenetic tree and other data files
├── 01_run_DADA2_16S_pseudo_V8.6.log
├── DADA2.Seqs_decontam.fa
├── DADA2.Seqs_decontam_filtered.fa
├── DADA2.Seqs.fa
├── DADA2.seqtab_nochim_decontam.tsv
├── DADA2.seqtab_nochim.RDS
├── DADA2.seqtab_nochim.tsv
├── DADA2.taxa_silva_decontam.tsv
├── DADA2.taxa_silva.tsv
├── DADA2.track_each.tsv
├── decontam_contaminants.csv
├── Ps_obj_decontam_filt3.Rds
├── Ps_obj_decontam.Rds
├── QualProf.pdf
├── Read1Errors.pdf
├── Read2Errors.pdf
└── Tree
├── DADA2.filter
├── DADA2.Seqs_decontam_filtered.filtered.align
├── DADA2.Seqs_decontam_filtered.filtered.align.bionj
├── DADA2.Seqs_decontam_filtered.filtered.align.iqtree
├── DADA2.Seqs_decontam_filtered.filtered.align.log
├── DADA2.Seqs_decontam_filtered.filtered.align.treefile
└── DADA2.Seqs_decontam_filtered.FT.tree
├── 00_cutadapt.log
├── 00_cutadapt_v2.0.sh
├── 01_DADA2_16S_merge_V8.6.R
├── 01_run_DADA2_16S_V8.6.sh
├── 02_Decontamination.html
├── 02_Decontamination.md
├── 02_Decontamination.Rmd
├── 03_Filter_taxa.html
├── 03_Filter_taxa.md
├── 03_Filter_taxa.Rmd
├── 04_calc_tree.log
├── 04_calc_tree_V2.0.sh
├── 05_Diff_abund.html
├── 05_Diff_abund.md
├── 05_Diff_abund.Rmd
├── Anaerobic_CUE.Rproj # R project file
├── AnCUE_Metadata.csv # Metadata file
├── AnCUE_Metadata_decontam.csv
├── DESeq2_byTime_a-0.05_LFC0-322.txt # DESeq2 results table
├── fems-microbiology-ecology.csl
├── LICENSE # Copyright information
├── README.md # Overview of the repo
└── references.bib # Bibtex formatted refereces cited in the RMD file
Viewing and reproducing the analysis
The MD files can be used to display the output on github, while HTML files can be used for offline viewing. The RMD files are best compiled using knitr on RStudio.