RNA-seq contamination with human mitochondrial sequence?

[BhariD]

Can we expect human mitochondrial sequence in Human RNA-seq library? I mean does the presence of mitochondrial sequence in RNA-seq data stands biological significance or likely a result of contamination?

I have over-represented sequences (>0.1% of total reads, up to 0.35%) in my RNA-seq library. Is this normal? Should I be excluding these "contaminating" sequences or leave them as they might reflect some expressed mitochondrial genes?

thoughts please?

[NextGenSeq]

Yes, we always see mtRNA in our RNA-Seq libraries. If you don't want it use Ribo-Zero Gold or oligo-dT priming.

Since mtRNA mutations are clinically significant I personally prefer having mtRNA in my libraries. The rRNA I could live without though.