Short paired-end reads trump long single-end reads for expression analysis.

ABSTRACT: BACKGROUND:Typical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be generated for the same cost, and it is not obvious which strategy should be preferred. Using publicly available data, we test whether short-paired end reads can achieve more robust expression estimates and differential expression results than single-end reads of approximately the same total number of sequenced bases. RESULTS:At both the transcript and gene

SUBMITTER: Freedman AH 

PROVIDER: S-EPMC7168855 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature