Impact of gene annotation choice on the quantification of RNA-seq data.

ABSTRACT:

Background

RNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to each gene. Gene annotation data, which include chromosomal coordinates of exons for tens of thousands of genes, are required for this quantification process. There are several major sources of gene annotations that can be used for quantification, such as Ensembl and RefSeq databases. However, there is very little understanding of the effect that the choice of annotation has on the accuracy of gene expression quantification in an RNA-seq analysis.

Results

In this paper, we present results from our comparison of Ensembl and RefSeq

SUBMITTER: Chisanga D 

PROVIDER: S-EPMC8969366 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature