I have been working on estimating the relative abundancy of selected bacterial strains in a metagenomic dataset, derived from whole genome sequencing using Illumina TruSeq kit + HiSeq sequencer. My thought is to do initial quality control using Trimmomatic, followed by mapping to reference bacterial genomes using Bowtie2. I read that I can merge forward and reverse reads before mapping, using tools like PEAR.
Now I am wondering if this merging step is recommended or not? Will this make the subsequent mapping more accurate?
Also, since I am quantifying reads mapped to each bacterial genome. Once I merge the reads and map, I should treat merged and unmerged reads differently in calculation. For example, One hit from a merged read should be counted twice, as compared to two hits from both forward and reverse reads. Am I right?
Thanks in advance!