RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods.

ABSTRACT: RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do n

SUBMITTER: Germain PL 

PROVIDER: S-EPMC4914128 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature