RNA-SeQC

What is RNA-SeQC?

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.

RNA-SeQC is built on the GATK as well as the Picard API.

See also

How do I get RNA-SeQC

How do I run RNA-SeQC

Publications

Citing RNA-SeQC

If you are using RNA-SeQC for your work, please cite the following paper:

Deluca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. (2012) RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics Manuscript

Related Publications

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A (2010) Nature Methods 7, 709-715.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20 (9):1297-303.

Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501.