I observe very often percentages as low as 30%. Of course, its hard to generalize but I would be interested in other people experiences. Do anybody observe any major mapping improvements when using certain mapping programms?
Specifically, I talk of aligning paired end mRNA reads (read length 100) to the genome (mus musculus). I have already seen several mRNA experiments and I have frequently observed such a low mapping efficiency when aligning the data with Bowtie.