Remove mitochondrial genome? RNA-Seq

[ileanadrt]

Hello! I'm working with CHO cells. I performed RNA-sequencing (on Illumina) for gene expression profiling.
After quality check and trimming, I downloaded the genome and mapped the reads with tophat. Then I realized that the reference genome file includes the mitochondrial genome as one scaffold. Should I remove it and map the reads again?
Thanks in advance

[SNPsaurus]

I don't think you should remove it. Right now, the mtRNA reads map correctly to the mtDNA scaffold. If you were to remove it, those mt reads would possibly find artifactual alignments to the nuclear sequences.

[ileanadrt]

Thank you for answering. I supposed that but I wasn't sure