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Transcriptomics and RNA-Seq Data Analysis

  • Xuhua Xia
Chapter

Abstract

High-throughput sequencing data (HTS) has been used in detecting not only differential gene expression, but also alternative splicing events and different transcription start and termination sites. It has also been used in ribosome profiling for characterizing translation efficiency and Hi-C method for constructing genome 3-D architecture. There are two main difficulties in analyzing HTS data: the large file size, often in terabytes, and the allocation of reads to paralogous genes which impacts the accuracy of computed RPKM values, especially for multicellular eukaryotes with many paralogues. This chapter provides a conceptual framework for analyzing HTS data and offers numerical illustrations of solutions to both problems mentioned above. It includes examples from real data on how to compare performance of different software packages.

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© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Xuhua Xia
    • 1
  1. 1.University of Ottawa CAREG and Biology DepartmentOttawaCanada

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