TY - JOUR
T1 - Identification of alternative splicing and polyadenylation in rna-seq data
AU - Dixit, Gunjan
AU - Zheng, Ying
AU - Parker, Brian
AU - Wen, Jiayu
N1 - Publisher Copyright:
© 2021 JoVE Journal of Visualized Experiments.
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85110428341&partnerID=8YFLogxK
U2 - 10.3791/62636
DO - 10.3791/62636
M3 - Article
SN - 1940-087X
VL - 2021
JO - Journal of Visualized Experiments
JF - Journal of Visualized Experiments
IS - 172
M1 - e62636
ER -