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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.See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

SUBMITTER: DeLuca DS 

PROVIDER: S-EPMC3356847 | biostudies-other | 2012 Jun

REPOSITORIES: biostudies-other

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

DeLuca David S DS   Levin Joshua Z JZ   Sivachenko Andrey A   Fennell Timothy T   Nazaire Marc-Danie MD   Williams Chris C   Reich Michael M   Winckler Wendy W   Getz Gad G  

Bioinformatics (Oxford, England) 20120425 11


<h4>Unlabelled</h4>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 an  ...[more]

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