a question for the percentage of aligned reads

[chenwb]

hi~
As I read from papers,I found SOLiD's reads which could be mapped to genome(or dataset) in RNA-seq is usually 50%~60% of total reads. In Prokaryotes whose transcriptome is almost as same as genome, the mapped reads is also ~ 60% of total reads.
Why are unmapped reads so much, even up to 50%? Are they errors? or the special colorspace format? or mapping tools bias?

Thanxx

[SeqAA]

Because there is no pre filtering of the SOLiD data. Other platforms filter out reads prior to mapping so you are mapping a reduced set of reads. Thus the mapping percentages are higher.