Transcriptomics and RNA-Seq Data Analysis
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.
- Li F, Ge P, Hui WH, Atanasov I, Rogers K, Guo Q, Osato D, Falick AM, Zhou ZH, Simpson L (2009) Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc Natl Acad Sci U S A 106(30):12306–12310CrossRefPubMedPubMedCentralGoogle Scholar
- Schena M (2003) Microarray analysis. Wiley-Liss, New YorkGoogle Scholar
- Smircich P, Eastman G, Bispo S, Duhagon MA, Guerra-Slompo EP, Garat B, Goldenberg S, Munroe DJ, Dallagiovanna B, Holetz F et al (2015) Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi. BMC Genomics 16:443PubMedPubMedCentralCrossRefGoogle Scholar
- Team GE (2011) Closure of the NCBI SRA and implications for the long-term future of genomics data storage. Genome Biol 12(3):402Google Scholar
- Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515CrossRefPubMedPubMedCentralGoogle Scholar
- Wei Y, Silke JR, Xia X (2017) Elucidating the 16S rRNA 3′ boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data. Sci Rep. https://doi.org/10.1038/s41598-017-17918-6