How much sequencing depth is required for RNA-seq experiments?

The sequence depth varies depending on the goals of the RNA-seq experiments. In general, most experiments require 5-200 million reads per sample. However, the sequencing depth is dependent on the organism complexity and size. Gene expression profiling experiments that look for a snapshot of highly expressed genes require only 5-25 million reads per sample. Experiments designed for an in-depth view of the transcriptome, or to assemble new transcripts require 100-200 million reads. Experiments designed for a wider view of gene expression and information on alternative splicing typically require 30-60 million reads per sample. Targeted RNA expression requires fewer reads. For example, Illumina recommends 3 million reads per sample for targeted RNA expression. miRNA or small RNA analysis may require even fewer reads than whole transcriptome sequencing, with 1-5 million reads per sample.