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. Researchers at the Tulane University School of Medicine present a protocol that 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.
SAM-format alignment files displayed on IGV
From top to bottom: RNA-Seq coverage and reads from both strands, RNA-Seq coverage and reads from the plus strand, RNA-Seq coverage and reads from the minus strand, and gene annotation (chrEBV_Akata_inverted.bed)
Availability – EBSeq is available at: http://www.bioconductor.org/packages/devel/bioc/html/EBSeq.html