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
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
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