title: RNA-Seq Analysis Pipeline Based on Oshell Environment.
abstract: Advances in transcriptome sequencing (RNA-Seq) have revolutionized the way to characterize and quantify transcripts. The breakthroughs in RNA-Seq technologies give rise to the ever-increasing volumes of data, making data processing the bottleneck of transcriptome research. It becomes crucial to develop an efficient analysis pipeline to automate RNA-Seq data analysis. Based on Oshell environment, we present here an ultra-fast and powerful RNA-Seq analysis pipeline for quality control, sequence alignment, variation detection, expression quantification and junction discovery. The pipeline runs on both Linux and Windows operating systems, with either stand-alone or cluster computing environment. Parallel computing is also supported for improved processing speed. Oshell is free for non-commercial use at http://omicsoft.com/oshell.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Jun
authors.initials: J
authors.lastname: Hu
authors.forename: Matthew
authors.initials: M
authors.lastname: Newman
authors.forename: Kejun
authors.initials: K
authors.lastname: Liu
authors.forename: Huanying
authors.initials: H
authors.lastname: Ge
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software