Whole genome sequencing for a bacterial strain for RNA sequencing

Hello,
I am new RNA sequencing work. I have raw fastq files (from extracted RNA and DNA both) for bacteria “Paucibacter toxinivorans strain IM4”. I am not able to find whole reference genome for the same bacteria. But, there is partial 16S sequence available at NCBI
www.ncbi.nlm.nih.gov/nuccore/1031488746

Do I first need to process DNA fastq files for whole genome sequencing and then move to RNA sequencing analysis? If not, Can I use the available partial 16S sequence for alignment?
Please can anybody guide me ?