After running some RNA-seq experiment, we have observed an over-represented sequence which do not correspond to any adapter used. It clearly seems to be a contaminant.
But my main question is why do I get this sequence only in one strand?
As I get the sequence in 2 400 000 reads, I don't get its reverse-complemented sequence. I don't know why, because if I get a contaminant sequence, I should get half of the reads with the sequence, and half with its complement, shouldn't I?