Hello everyone, I have a dataset of differentially expressed miRNAs.
I aligned my microRNA reads (10 millions per sample aprox) against reference genome, obtaining an average of 7.5 million aligned read per sample, and used FeatureCounts from RSubRead to count them asigning to reference miRNA GTF in miRBase, obtaining an average of 60% of asignment. Then, I used DESeq2 to perform differential expression analysis.
As said in Mullokandov et al. (2013), functional miRNAs should only be considered when expressed above 100-1000 RPM on average. I calculated CPM from FeatureCounts counts file and obtained average expression per group (2 groups contast) and expression per sample.
I would like to know if there is any difference between the concept of RPM and CPM, as I think the are quite the same, but not sure about that. I assumed miRNAs with a cpm expression below 100 to be spurious and noise, but I would like to be sure about that.
Any suggestions and clarifications?