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 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 abundances of GO-terms.
· Statistical analysis of the groups
· Pathway analysis on the differential abundance analysis using MetaCyc database.
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