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.
Can we have some details abou the reads (length, paired, not)? What aligner are you using? What organism? What reference sequences are you using, genome or transcriptome?
In bacterial samples I have seen mapping rates of up to 80-90%. Depends possibly on many factors, but 30% seems very low. Your sample is maybe contaminated, or your parameters too strict. Other than that I have good experience with BFAST and mosaic.
Your question is hard to address without asking "align at what stringency?" Are you asking "what percentage of reads should be unique alignment of high quality"? I'm doing a RNS-seq analysis right now, and a significant minority of my reads come from repetitive regions that do not have a unique alignment.