I have received recently eight RNA-seq samples. We know that the reads are
reversely stranded. After aligning those samples to their reference genome, I run
infer_experiment on the alignment data just to make sure everything is fine.
Five samples out of eight showed that they are really
reversely stranded, however, the remaining three samples showed that the reads are
forward stranded. In addition, those three samples show that they contain high percentage of
rRNA sequences (using
bbduk ~30 percent of the reads).
Removing those reads did not change the result of
So what could be the reason(s) behind such confusion? Thank you in advance.