The CloVR-Metatranscriptomics track provides a robust initial analysis of community-wide microbial gene expression from cDNA sequences. The major components of this protocol are:
A) UCLUST – a C++-based software package for clustering redundant DNA and peptide sequences.
D) Additional statistical and graphical evaluation within the pipeline includes Metastats and custom R scripts implemented in CloVR.
The CloVR-Metatranscriptomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file for comparative analysis. This track generates several output reports including taxonomic and functional abundance tables, independent analysis of rRNA sequences, statistical comparisons of feature abundances between user-defined populations, and heatmaps with unsupervised clusterings of all samples.
Executing this pipeline is identical to the original CloVR-Metagenomics walkthrough — simply substitute the following config file: