Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment.

ABSTRACT:

Background

RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies t

SUBMITTER: Shrestha AMS 

PROVIDER: S-EPMC8815227 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature