RNA-SeQC: RNA-seq metrics for quality control and process optimization

TLDR

RNA‑seq enables transcriptome‑wide profiling, but assessing sequencing performance and library quality is essential and few tools exist. The study introduces RNA‑SeQC, a program that provides key measures of RNA‑seq data quality. RNA‑SeQC computes metrics such as yield, alignment and duplication rates, GC bias, rRNA content, exon/intron coverage, 3′/5′ bias, and transcript detectability, and supports multi‑sample evaluation and pipeline integration. RNA‑SeQC enables researchers to make informed sample‑inclusion decisions and supports experiment design, process optimization, and downstream analysis. RNA‑SeQC is available online at Genepattern.org and as a command‑line tool at broadinstitute.org/rna‑seqc, with contact [e-mail] and supplementary data online.

Abstract

Abstract Summary: RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3′/5′ bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool. Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.