I am using miRDeep2 to analyze my small RNA sequencing data. The quantifier.pl module outputs read counts and normalized read counts for miRNA within each sample. I believe the normalization is done against total reads, but I am not sure. Can somebody point me to documentation on how the MiRDeep2 normalizes data.
Are there different ways to normalize small RNA data. My experiment targets small RNA biogenesis factors so I am concerned about normalizing to total reads since I might expect that to be different across my different cell lines.
Thank you!
Are there different ways to normalize small RNA data. My experiment targets small RNA biogenesis factors so I am concerned about normalizing to total reads since I might expect that to be different across my different cell lines.
Thank you!