Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species.

ABSTRACT:

Background

The usual analysis of RNA sequencing (RNA-seq) reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-seq analysis workflow on the recovery of useful processed data available for downstream analysis.

Findings

At the preprocessing step, w

SUBMITTER: Paya-Milans M 

PROVIDER: S-EPMC6275443 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature