Hi all,
We are having a lab debate regarding short RNA sequence. Specifically, we generally we do unique mapping of the reads to the genome. After intersecting the mapped reads to the miRNAs and other short RNAs we want to calculate a RPM value. My lab mate wants to normalize the expression to the total number of raw reads (total off of the machine). Me, on the other hand thinks that we should be normailzing to the total number of mapped reads.
Can someone possible way in on this...
We are having a lab debate regarding short RNA sequence. Specifically, we generally we do unique mapping of the reads to the genome. After intersecting the mapped reads to the miRNAs and other short RNAs we want to calculate a RPM value. My lab mate wants to normalize the expression to the total number of raw reads (total off of the machine). Me, on the other hand thinks that we should be normailzing to the total number of mapped reads.
Can someone possible way in on this...
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