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Review
. 2018 Mar;11(2):153-161.
doi: 10.1111/cts.12511. Epub 2017 Oct 23.

Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research

Ana Caroline C Sá  1   2 , Wolfgang Sadee  3 , Julie A Johnson  1   2   4
Affiliations
Review

Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research

Ana Caroline C Sá et al. Clin Transl Sci. 2018 Mar.
No abstract available

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Figures

Figure 1
Figure 1
Schematic representation of the pre‐messenger RNA (mRNA), with exons and introns, and the RNA‐Sequencing (RNA‐Seq) short reads mapped to the final m(RNA).
Figure 2
Figure 2
Genome‐based assembly strategy for reconstructing transcripts from RNA‐Seq reads. First, short RNA‐Seq reads are aligned to the reference genome, accounting for possible splicing events. Then transcripts are reconstructed from the spliced alignments. The colors of the RNA‐Seq reads represent the transcript isoform from which they are derived.
Figure 3
Figure 3
RNA‐Seq can also be used to interrogate allelic effects, in sites with a polymorphism confirmed by dense coverage of reads. Based on the reads aligned to a specific genome locus, it is possible to calculate the ratio of reads from each allele (allele 1: allele 2). Allele‐specific expression (ASE) is determined if the calculated ratio deviates from the expected 50:50.
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