Hi everyone, I'm mapping mRNA-seq data (single end, 40bp) of C.elegans to the cDNA reference (junction of exons) with bowtie, I'm a beginner for RNA-seq data analysis, so I didn't use Tophat or other specific tools for RNA-seq. The cDNA reference is downloaded from Ensembl dataset.
I was wondering that should the RNA-seq reads only be mapped to one strand of the reference (either +strand or - strand since the sequence of mRNA is same as the cDNA reference)? However, my mapping result shows that reads could be mapped to both strands, shall I eliminate the mapped reads on one strand because there may be contaminations? Thanks.