Analysis of EBV Transcription Using High-Throughput RNA Sequencing

• DOI: 10.1007/978-1-4939-6655-4_7
• Publication Date: 2016-11-21T20:25:45Z
• Authors: Tina O’Grady; Melody Baddoo; Erik K. Flemington
• Keywords: Gene Expression Regulation, Viral; Herpesvirus 4, Human; 0303 health sciences; Sequence Analysis, RNA; Gene Expression Profiling; Computational Biology; High-Throughput Nucleotide Sequencing; Genome, Viral; Genomics; Web Browser; 3. Good health; 03 medical and health sciences; Humans; Transcriptome; Software

High-throughput sequencing of RNA is used to analyze the transcriptomes of viruses and cells, providing information about transcript structure and abundance. A wide array of programs and pipelines has been created to manage and interpret the abundance of data generated from high-throughput RNA sequencing experiments. This protocol details the use of free and open-source programs to align RNA-Seq reads to a reference genome, visualize read coverage and splice junctions, estimate transcript abundance, and evaluate differential expression of transcripts in different conditions. Particular concerns related to EBV and viral transcriptomics are addressed and access to EBV reference files is provided.