How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq

• DOI: 10.1371/journal.pone.0130262
• Publication Date: 2015-06-24T18:09:46Z
• Authors: Luis Fernando Gar...; Octavio Martínez
• Keywords: RNA-Seq

RNA-seq experiments estimate the number of genes expressed in a transcriptome as well their relative frequencies. However, an undetermined can remain undetected due to low expression sample size (sequence depth). Estimation true is essential order determine which are exclusively specific tissues or under particular conditions. A reliable also required accurately measure changes and predict sequencing depth needed increase proportion detected genes. This problem analogous ecological sampling problems such estimating species at given site. Here we present non-parametric estimator for extra detect Our estimators superior ones already published by having smaller standard errors biases. We applied our method set 32 publicly available experiments, including evaluation 311 individually sequenced libraries. found that majority cases more than one thousand undetected, on average approximately 6% per accession undetected. figure increases 10% if individual libraries analyzed. applicable metagenomic experiments. Using method, them be calculated, leading accurate complete gene studies.