RNA-Seq Analysis Pipeline Based on Oshell Environment

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, developers at Omicsoft Corporation 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.


RNA-Seq pipeline in Oshell environment. Oshell project environment is created by initiation and closing of project. Inside the project are input files, analysis modules (orange) and outputs. If the BAM files, aligned by MapRnaSeqReadsToGenome or imported by AddGenomeMappedRnaSeqReads, contain both mapped and unmapped reads, the unmapped reads can be processed in fusion detection to find junction-spanning reads. Table reports and figures generated by analysis modules can be exported as TXT and PDF files.

Availability – Oshell is free for non-commercial use at http://omicsoft.com/oshell

Jing Li, Jun Hu, Newman M, Kejun Liu, Huanying Ge. (2015) RNA-Seq Analysis Pipeline Based on Oshell Environment. IEEE/ACM Trans Comput Biol Bioinform 11(5):973-8. [abstract]

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