We used miseq RNA sequencing to estimate the host cell pathogen ratio. The size of pathogen genome is 810^6 bp. The size of human genome is 1.510^9 bp. The size of pathogen extron is 8*10^6 bp. The size of human extron is 10^8 bp. By analysising the data using Kallisto, we found that the ratio of pathogen to host reads is about 1 to 500 using unfiltered data.
(In the infection experiment: host:pathogen= 2:1)