I have two bacteria rna sequenced together, after data cleaning, I used bowtie2 to map the reads against two bacteria genome seperately. I got a total 86% (35%+51%) alignment rate of the two bacteria when using --very-sensitive-local; and a total of 81% (33%+48%) alignment rate when using --very-sensitive-end-to-end. The reason why it doesn't ammount to 100% is that the rna was extracted together with two bacteria and one fungus in the system, after extraction, fungi rna was fished out, so the bacterial rna was left with a bit fungi rna.
My questions is: which mode gives more accurate results? I understand that both local and end-to-end modes will give some false alignment. Is there a genernal undstanding that which one is more accurate?