title: Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.
abstract: QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. It comprises two main sections. First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC. Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool. Second is the QC database, which displays the resulting metrics in a user-friendly web interface. It was designed to allow users with less computational experience to easily generate and view QC information for their data, to investigate individual samples and aggregate reports of sample groups, and to sort and search samples based on quality. The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. The source code for not-for-profit use and a fully functional sample user interface with mock data are available at http://bioserv.mps.ohio-state.edu/QuaCRS/.
authors.affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Karl W
authors.initials: KW
authors.lastname: Kroll
authors.affiliation: Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Nima E
authors.initials: NE
authors.lastname: Mokaram
authors.affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pelletier
authors.affiliation: Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Frankhouser
authors.affiliation: Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Maximillian S
authors.initials: MS
authors.lastname: Westphal
authors.affiliation: Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Paige A
authors.initials: PA
authors.lastname: Stump
authors.affiliation: Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Cameron L
authors.initials: CL
authors.lastname: Stump
authors.affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. ; Department of Physics, The Ohio State University, Columbus, OH, USA. ; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA. ; Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
authors.affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: James S
authors.initials: JS
authors.lastname: Blachly
authors.affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. ; Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Pearlly
authors.initials: P
authors.lastname: Yan
keywords: FastQC; RNA-SeQC; RNA-seq; RSeQC; database; quality control