Methods for analyzing next-generation sequencing data III. From setting a Linux environment to manipulating Lactobacillus RNA-seq data

Abstract

There are many prerequisites for NGS data analysis on Linux system. We describe basic usage and commands on Linux environment. This includes the setting of Bio-Linux as a virtual machine, shared folders, and understanding of hardware requirements for NGS analysis. We show how to get a Lactobacillus genome sequences on Ensembl database and transcriptome data (bzipped FASTQ files) on DDBJ SRA. Many tasks on NGS analysis can effectively be performed by combining some Linux command line facilities, such as pipe and redirection.