Negative binomial additive model for RNA-Seq data analysis

摘要

In recent years, RNA-Seq experiments have become the state-of-the-art method for quantifying mRNAs levels by measuring gene expression digitally in biological samples. An RNA-Seq experiment usually starts with isolating RNA sequences from biological samples using the Illumina Genome Analyzer, a commonly used platform for high-throughput sequencing data. These mRNA sequences are reverse transcribed into cDNA fragments. To reduce the sequencing cost and increase the speed of reading the cDNA fragments (typically a few thousands bp), these fragments are sheared into short reads (50-450 bp). These reads are mapped back to the original reference genomes/transcriptomes and the number of read counts mapping to each gene/transcript region are computed. RNA-Seq experiments are usually summarized as a count table with each row representing a gene/transcript and each column representing a sample.