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

Bioinformatics
Authors
Keywords
Abstract

UNLABELLED: 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.

Year of Publication
2012
Journal
Bioinformatics
Volume
28
Issue
11
Pages
1530-2
Date Published
2012 Jun 01
ISSN
1367-4811
URL
DOI
10.1093/bioinformatics/bts196
PubMed ID
22539670
PubMed Central ID
PMC3356847
Links
Grant list
R01 GM074024 / GM / NIGMS NIH HHS / United States