Impact of human gene annotations on RNA-seq differential expression analysis.

ABSTRACT:

Background

Differential expression (DE) analysis of RNA-seq data typically depends on gene annotations. Different sets of gene annotations are available for the human genome and are continually updated-a process complicated with the development and application of high-throughput sequencing technologies. However, the impact of the complexity of gene annotations on DE analysis remains unclear.

Results

Using "mappability", a metric of the complexity of gene annotation, we compared three distinct human gene annotations, GENCODE, RefSeq, and NONCODE, and evaluated how mappability affected DE analysis. We found that mappability was significantly different among the human gene annotations. We also found that increasing mappability improved the performance of DE analysis, and the im

SUBMITTER: Hamaguchi Y 

PROVIDER: S-EPMC8501603 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature