Metatranscriptomic response of the wheat holobiont to decreasing soil water content

<p><strong>Background</strong></p> <p>This dataset contains processed high throughput metatranscriptomics (RNA) sequencing data related to the scientific article entitled&nbsp;<em>Metatranscriptomic response of the wheat holobiont to decreasing soil water content</em>.&nbsp;</p> <p>The files available in this archive are described below:</p> <p><strong>Contigs abundance:</strong><br> contigs/qc_mapping_stats.tsv<br> Contains read counts through various steps of the pipeline. &nbsp;</p> <p>contigs/merged_contigs_abundance.tsv<br> Number of reads that mapped to each contig for each sample. Rows = contig ID; column = sample ID.</p> <p>contigs/merged_contigs_abundance_cpm.tsv<br> Normalized (edgeR) number of reads (Count Per Million - CPM) that mapped to each contig for each sample. Rows = contig ID; column = sample ID.</p> <p><strong>Gene abundance:</strong><br> genes/merged_gene_abundance.tsv<br> Number of reads that mapped to each gene for each sample. Rows = gene ID; column = sample ID.</p> <p>genes/merged_gene_abundance_cpm.tsv<br> Normalized (edgeR) number of reads (Count Per Million - CPM) that mapped to each gene for each sample. Rows = gene ID; column = sample ID.</p> <p><strong>Beta diversity:</strong><br> Beta diversity tables computed (with microbiomeutils v0.9) on gene abundance and contig abundance and bacteria/archaea contigs abundance are available here:<br> betadiv/bray_curtis_contig_abundance/<br> betadiv/bray_curtis_gene_abundance/<br> betadiv/bray_curtis_contig_bacteriaArchaea/<br> Inside each of these directory is an index.html file allowing to visualize an Emperor interactive 3d vizualisation of beta diversity ordinations.<br> ./3d_bray_curtis_plot/index.html</p> <p><strong>Functional annotations:</strong><br> Gene functional annotations procedures are inspired from the JGI annotation workflow and is described in PMID: 31600863.</p> <p>annotations/annotations.tsv<br> Functional annotations and taxonomic lineages (see below) are merged in a single tabular separated file.&nbsp;<br> Contains the results of&nbsp;<br> DIAMOND BLASTp of each gene amino acid sequence against KEGG genes database.<br> DIAMOND BLASTp of each gene amino acid sequence against NCBI nr database.<br> HMMSCAN of each gene amino acid sequence against PFAM-A database (in domtblout format).<br> HMMSCAN of each gene amino acid sequence against PFAM-A database (in tblout format).<br> RPS-BLAST of each gene amino acid sequence against COG database.</p> <p><br> <strong>Contigs-based taxonomy:</strong></p> <p>consensus/taxonomy.tsv<br> Contains the taxonomy assignment for each contig. Taxonomy assignment was performed with PMID : 31640809.&nbsp;<br> consensus/feature_table_&lt;normalized&gt;_L1 to _L7.txt<br> Contigs abundance tables of each contig for each sample. Taxonomy assignment was performed with PMID : 31640809.&nbsp;</p> <p>consensus/feature_table.tsv<br> Contains the raw reads abundance of each contig across all samples.</p> <p>consensus/feature_table_normalized.tsv<br> Contains the normalized (with edgeR) reads abundance of each bin across all samples.</p> <p>&nbsp;</p>