Identification of alternative splicing and polyadenylation in rna-seq data

Gunjan Dixit, Ying Zheng, Brian Parker, Jiayu Wen*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    2 Citations (Scopus)

    Abstract

    As well as the typical analysis of RNA-Seq to measure differential gene expression (DGE) across experimental/biological conditions, RNA-seq data can also be utilized to explore other complex regulatory mechanisms at the exon level. Alternative splicing and polyadenylation play a crucial role in the functional diversity of a gene by generating different isoforms to regulate gene expression at the post-transcriptional level, and limiting analyses to the whole gene level can miss this important regulatory layer. Here, we demonstrate detailed step by step analyses for identification and visualization of differential exon and polyadenylation site usage across conditions, using Bioconductor and other packages and functions, including DEXSeq, diffSplice from the Limma package, and rMATS.

    Original languageEnglish
    Article numbere62636
    JournalJournal of Visualized Experiments
    Volume2021
    Issue number172
    DOIs
    Publication statusPublished - 2021

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