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

ABSTRACT:

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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

SUBMITTER: DeLuca DS 

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

REPOSITORIES: biostudies-literature