I've a bunch of small RNA-Seq samples that I aligned using bowtie. Surprisingly I found some traces of mRNA expression in the alignment (reads aligning on mRNA exons). especially mRNA highly expressed (e.g. MYC). Is it normal ? I use Illumina TruSeq small RNA kit without gel excision. RNA 3' adapter is specifically modified to target microRNAs and other small RNAs that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Thus I do not expect mRNA traces in my data ...
Anyone experiences such thing ?