We have some E coli. total RNA-seq data and my PI would like to count the percentage of messenger RNA and ribosomal RNA in the data. My idea is mapping the data to the transcriptome and rRNA data separately and then count the reads#.
Do you think this is a doable plan? But, I have no idea where to find the transcriptome and rRNA reference for the E coli.
Is there is an alternate way to do this analysis? Any suggestion will be appreciated.