What you will learn
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.
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References
Dobin A, Gingeras TR. Optimizing RNA-Seq mapping with STAR. Methods Mol Biol. 2016;1415:245–62.
Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9(8):e1003118.
Acknowledgements
We are grateful to Dr. Richa Barthi (Bioinformatician at TUM Campus Straubing, Germany) for critically reading this text. We thank for correcting our mistakes and suggesting relevant improvements to the original manuscript.
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Kappelmann-Fenzl, M. (2021). Reference Genome. In: Kappelmann-Fenzl, M. (eds) Next Generation Sequencing and Data Analysis. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-030-62490-3_8
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DOI: https://doi.org/10.1007/978-3-030-62490-3_8
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