title: RNA-SeQC: RNA-seq metrics for quality control and process optimization.
abstract: 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.
  
  
  METHODS
  See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA. ddeluca@broadinstitute.org
authors.forename: David S
authors.initials: DS
authors.lastname: DeLuca
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Andrey
authors.initials: A
authors.lastname: Sivachenko
authors.forename: Timothy
authors.initials: T
authors.lastname: Fennell
authors.forename: Marc-Danie
authors.initials: MD
authors.lastname: Nazaire
authors.forename: Chris
authors.initials: C
authors.lastname: Williams
authors.forename: Michael
authors.initials: M
authors.lastname: Reich
authors.forename: Wendy
authors.initials: W
authors.lastname: Winckler
authors.forename: Gad
authors.initials: G
authors.lastname: Getz
mesh_terms: D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D011786:Quality Control; D012313:RNA / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012335:RNA, Ribosomal; D012313:RNA