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.

B) BLASTN for preliminary screening of rRNA sequences using the full SILVA rRNA database.

C) BLASTX and BLASTN for functional and taxonomic assignment of non-ribosomal cDNA sequences, respectively.

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:

File: CloVR-Metatranscriptomics config file