I am hoping to get some insight into what is happening here or any suggestions.
I am aligning total RNA-seq, single-end data to S. pombe with STAR and Tophat but getting two very different uniquely mapping statistics:
Number of input reads | 20416529 Average input read length | 47 UNIQUE READS: Uniquely mapped reads number | 2622002 Uniquely mapped reads % | 12.84% Average mapped length | 48.83
Reads: Input : 20416529 Mapped : 19397908 (95.0% of input) 95.0% overall read mapping rate.
12.84 v 95% is a pretty big difference.