Methods for analyzing next-generation sequencing data XIV. RNA-seq analysis (Part 2)

Abstract

Lactobacillus rhamnosus is a probiotic lactic acid bacterium frequently isolated from human gastrointestinal mucosa of healthy individuals. We describe an analysis procedure to RNA-seq data (SRP125628 or GSE107337) on the acid stress response of L. rhamnosus GG on an integrated data analysis environment called Galaxy. Specifically, we will describe importing FASTQ files from the public database ENA to Galaxy, preprocessing using Trimmomatic, mapping to reference genome sequence using Bowtie2, and obtaining count data using htseq-count. We will also discuss about similarities of count data between the original and ours. Supplementary materials are available online at: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq2.html#about_book_JSLAB.