Metatranscriptomic response of the wheat holobiont to decreasing soil water content

Background

This dataset contains processed high throughput metatranscriptomics (RNA) sequencing data related to the scientific article entitled Metatranscriptomic response of the wheat holobiont to decreasing soil water content. 

The files available in this archive are described below:

Contigs abundance:
contigs/qc_mapping_stats.tsv
Contains read counts through various steps of the pipeline.  

contigs/merged_contigs_abundance.tsv
Number of reads that mapped to each contig for each sample. Rows = contig ID; column = sample ID.

contigs/merged_contigs_abundance_cpm.tsv
Normalized (edgeR) number of reads (Count Per Million - CPM) that mapped to each contig for each sample. Rows = contig ID; column = sample ID.

Gene abundance:
genes/merged_gene_abundance.tsv
Number of reads that mapped to each gene for each sample. Rows = gene ID; column = sample ID.

genes/merged_gene_abundance_cpm.tsv
Normalized (edgeR) number of reads (Count Per Million - CPM) that mapped to each gene for each sample. Rows = gene ID; column = sample ID.

Beta diversity:
Beta diversity tables computed (with microbiomeutils v0.9) on gene abundance and contig abundance and bacteria/archaea contigs abundance are available here:
betadiv/bray_curtis_contig_abundance/
betadiv/bray_curtis_gene_abundance/
betadiv/bray_curtis_contig_bacteriaArchaea/
Inside each of these directory is an index.html file allowing to visualize an Emperor interactive 3d vizualisation of beta diversity ordinations.
./3d_bray_curtis_plot/index.html

Functional annotations:
Gene functional annotations procedures are inspired from the JGI annotation workflow and is described in PMID: 31600863.

annotations/annotations.tsv
Functional annotations and taxonomic lineages (see below) are merged in a single tabular separated file. 
Contains the results of 
DIAMOND BLASTp of each gene amino acid sequence against KEGG genes database.
DIAMOND BLASTp of each gene amino acid sequence against NCBI nr database.
HMMSCAN of each gene amino acid sequence against PFAM-A database (in domtblout format).
HMMSCAN of each gene amino acid sequence against PFAM-A database (in tblout format).
RPS-BLAST of each gene amino acid sequence against COG database.

Contigs-based taxonomy:

consensus/taxonomy.tsv
Contains the taxonomy assignment for each contig. Taxonomy assignment was performed with PMID : 31640809. 
consensus/feature_table__L1 to _L7.txt
Contigs abundance tables of each contig for each sample. Taxonomy assignment was performed with PMID : 31640809. 

consensus/feature_table.tsv
Contains the raw reads abundance of each contig across all samples.

consensus/feature_table_normalized.tsv
Contains the normalized (with edgeR) reads abundance of each bin across all samples.