Using CLC Genomics Workbench, we will go through a pipeline for analyzing metatranscriptome NGS data from microbial communities and perform pathways interpretation on it.
- Import "raw" NGS sequencing data and prepare the samples for analysis
- Find relevant annotated genomes with a curated reference database while removing ribosomal RNA with the SILVA database (database of rRNAs)
- De novo assemble the unclassified reads into contigs to also find transcripts of taxa not present in the reference database
- Map the reads to the assembled contigs and database · Build a functional profile of the samples to get an abundance of GO-terms.
- Statistical analysis of the groups
- Pathway analysis on the differential abundance analysis using MetaCyc database.
