Transcript Assembly and Annotations: Bias and Adjustment.

ABSTRACT:

Motivation

Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodologies and information resources can lead to significant differences. It has been demonstrated that the choice of annotation can have a significant impact on gene expression analysis. Furthermore, transcript assembly is closely linked to annotations, as assembling large-scale available RNA-seq data is an effective data-driven way to construct annotations, and annotations are often served as benchmarks to evaluate the accuracy of assembly methods. However, the influence of different annotations on transcript assembly is not ye

SUBMITTER: Zhang Q 

PROVIDER: S-EPMC10153229 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature