Reference Genome
8
Melanie Kappelmann-Fenzl
Contents
8.1 Introduction . . . . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. 106
8.2 Generate Genome Index via STAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
8.3 Generate Genome Index via Bowtie2 .. . . .. . .. . .. . . .. . .. . .. . . .. . .. . .. . . .. . .. . .. . . .. . .. . .. . . .. 108
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
What You Will Learn in This Chapter
This chapter describes the relevance of the reference genome for the analysis of Next
Generation Sequencing (NGS) data and how the respective reference genome can be
created. You will learn which databases provide the files for the creation of a
Reference Genome Index and which criteria you have to consider when choosing
the database and the respective files. Depending on the chosen alignment tool to be
used for further analyses, a Reference Genome Index must also be created with the
same tool. The corresponding code is shown in detail using the alignment software
tools STAR and Bowtie2.
M. Kappelmann-Fenzl (*)
Deggendorf Institute of Technology, Deggendorf, Germany
Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg,
Erlangen, Germany
e-mail: melanie.kappelmann-fenzl@th-deg.de
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3_8
105
8
Melanie Kappelmann-Fenzl
Contents
8.1 Introduction . . . . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. 106
8.2 Generate Genome Index via STAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
8.3 Generate Genome Index via Bowtie2 .. . . .. . .. . .. . . .. . .. . .. . . .. . .. . .. . . .. . .. . .. . . .. . .. . .. . . .. 108
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
What You Will Learn in This Chapter
This chapter describes the relevance of the reference genome for the analysis of Next
Generation Sequencing (NGS) data and how the respective reference genome can be
created. You will learn which databases provide the files for the creation of a
Reference Genome Index and which criteria you have to consider when choosing
the database and the respective files. Depending on the chosen alignment tool to be
used for further analyses, a Reference Genome Index must also be created with the
same tool. The corresponding code is shown in detail using the alignment software
tools STAR and Bowtie2.
M. Kappelmann-Fenzl (*)
Deggendorf Institute of Technology, Deggendorf, Germany
Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg,
Erlangen, Germany
e-mail: melanie.kappelmann-fenzl@th-deg.de
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3_8
105