Methods for analyzing next-generation sequencing data XV. RNA-seq analysis (Part 3)

Abstract

Galaxy is an integrative data analysis environment run on the web browser. As before, we explain a topic to quantify RNA expression from an RNA-seq dataset (GSE107337) which examined the acid stress response of Lactobacillus rhamnosus GG. First, we describe a preprocessing of annotation file with GFF format and extract nucleotide sequence information of the gene regions on the genome. Next, we obtain both count and TPM values for individual genes using the Kallisto quant program. Lastly, we compare the current results with those obtained from the original study and our previous ones. Supplementary materials are available online at: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq2.html#about_book_JSLAB.