RNA-SeQC specifications


Unique identifier OMICS_01234
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1.8
Stability Stable
Maintained Yes



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  • person_outline David DeLuca <>

RNA-SeQC article

RNA-SeQC citations

PMCID: 5800601

[…] aligner (version 2.3) [33] against the mm10 genome available at ftp://ftp.ensemble.org/pub/release-75/fasta/mus_musculus/dna/. rna-seq quality metrics controls were accessed by the broad institute’s rna-seqc tool [34]. read quantification was carried out with featurecounts [35]. read normalization and differential expression testing were performed with deseq package in r [36], and sequence data […]

PMCID: 5099203

[…] cd19+ b cells (n=16 patients, n=23 controls) was conducted using the truseq stranded mrna sample preparation kit followed by sequencing on a hiseq2500 instrument (illumina). qc was conducted using rna-seqc.25 reads were mapped with tophat2 and analysis of differential gene expression was performed using the cufflinks pipeline.26 27, methylation levels were tested in plink for genotype […]

PMCID: 4768675

[…] the most recent sequencing efforts for corals, but this is likely an indication of the low number of total sequence reads rather than sequence quality. high quality of short reads is demonstrated by rna-seqc results, which compare the raw sequence reads to trimmed and clipped sequences used as the input for assembly by trinity (supplemental informations 1 and 2). collectively, these results […]

RNA-SeQC institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA
RNA-SeQC funding source(s)
Supported by the Federal funds from the National Human Genome Research Institute, National Institutes of Health, Department of Health and Human under Contract No. HHSN268201000029C.

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