Hi, I have clinical urine samples from which i need to identify the gene expression changes in the pathogen after treatment. (i know the bacteria present in urine through urine culture test)
Q1. Should I do 16s DNA sequencing to identify the strain of the bacteria? How do I know the genes present in the DNA? Can I do annotation of the data and identify the genes to see which genes are virulent or responsible for biofilm formation?
Q2. I will be doing Rna-Seq to identify the expression of the genes. Do i need to provide the reference genome as the one sequenced above?
Do I need to do DNA sequencing and rna expression profiling to make my data look validated? What exactly is the right route to go to conclude my result.
Totally confused, I am new to this and this is my first bioinformatics clubbed project.