When sequencing RNA from freshly harvested tissues under proper conditions, you should generally expect > 50% mapped reads. In fact, everything < 80% would usually raise concerns.
From your description (in the question and comments) it sounds as if your samples are potentially degraded and therefore saturated with short RNA fragments, either because you’ve got old tissue, you’re looking at environmental samples, or from improper handling.
And since you’re not performing any enrichment, the sequencing data will then be highly saturated with degraded RNA, too. The reason for this is that RNA-seq is a (hopefully somewhat uniform) sampling of your sample aliquot: everything in it is proportionally represented in the RNA-seq data. That’s why enrichment steps are important, to increase the proportion of whatever fraction we’re interested in.
In particular,
- Total RNA is mostly composed of genes with many copies: mostly rRNA and (much less) tRNA. Hence the importance of ribosome depletion or poly(A) selection.
- RNA in general is unstable. Depending on the sample collection (non-tissue sample origin? age of the tissue before harvesting?), a large fraction of the RNA may have degraded into minuscule fragments, which are further shortened by the library preparation. Size selection would get rid of these undesired fragments.
In my experience, the second issue is exacerbated on certain sequencers (I’ve seen it on an Illumina HiSeq 1500) because a mixed library of short and long RNA doesn’t seem to cycle well through the whole fragment length. So even if you have a (small but still present) fraction of long RNA fragments, the sequencer may not be able to synthesise their whole length efficiently. The effect is that there are proportionally more short reads than there were short fragments in the sample.
You can verify this by calculating the insert size distribution of your reads after adapter trimming (e.g. using picard, or by simply tallying read lengths1). Small reads (< ~14 nt) from degradation fragments are essentially unmappable, since they are too short to have a specific identity. Even if we allowed the mapper to align them their coordinates would be essentially random.
1 This works:
awk 'NR % 4 == 2 {c[length($0)]++} END {for (i in c) print i, c[i]}' in.fastq