title: Analysis of EBV Transcription Using High-Throughput RNA Sequencing.
abstract: 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.
authors.affiliation: Department of Pathology, Tulane University School of Medicine, 1430 Tulane Avenue, Box SL-79, New Orleans, LA, 70112, USA.
authors.forename: Tina
authors.initials: T
authors.lastname: O'Grady
authors.affiliation: Department of Pathology, Tulane University School of Medicine, 1430 Tulane Avenue, Box SL-79, New Orleans, LA, 70112, USA.|Tulane Cancer Center, New Orleans, LA, USA.
authors.forename: Melody
authors.initials: M
authors.lastname: Baddoo
authors.affiliation: Department of Pathology, Tulane University School of Medicine, 1430 Tulane Avenue, Box SL-79, New Orleans, LA, 70112, USA. erik@tulane.edu.|Tulane Cancer Center, New Orleans, LA, USA. erik@tulane.edu.
authors.forename: Erik K
authors.initials: EK
authors.lastname: Flemington
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D004854:Herpesvirus 4, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome; D064878:Web Browser
keywords: Differential expression; EBSeq; Epstein-Barr virus; IGV; Integrative genomics viewer; RNA-Seq; RSEM; STAR; Transcriptomics