Comparative evaluation of full-length isoform quantification from RNA-Seq.

ABSTRACT:

Background

Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short.

Results

Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control.

Conclusions

Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on ideal

SUBMITTER: Sarantopoulou D 

PROVIDER: S-EPMC8145802 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature