An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

ABSTRACT: RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules

SUBMITTER: Wang Z 

PROVIDER: S-EPMC4972086 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature