Overview:1. Filter DNA reads by quality and host (e.g. for mouse gut bacteria we would filter low-quality reads AND reads that belong to mice)2. Align DNA reads (fastq, fasta) to Patric database (bacteria genomes) with taxoner (a bowtie2-based linux program) >> Get bacterial genomes3. Filter out low-quality alignments >> Bacterial genomes4. Filter RNA reads by quality5. Align RNA reads to bacterial genomes from step 3 >> RNA counts of genes6. Get pathway information >> RNA counts per KEGG pathwayIf you have treatment groups, we will be able to see changes in bacterial abundance as well as changes to RNA counts