RNA-SeQC protocols

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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 <>

Publication for RNA-SeQC

RNA-SeQC in pipelines

PMCID: 5268473
PMID: 28125622
DOI: 10.1371/journal.pone.0169614

[…] rnaseq data are available from the ncbi gene expression omnibus under the accession numbers gse55536., rnaseq data were aligned to the hg19 reference genome using star 2.3.0e[] with default options. rna-seqc[] was used to assess quality of each sample. estimated gene expression levels from pre- to post-lps were quantified as fragments per kilobase per million fragments mapped (fpkm), […]

PMCID: 5359597
PMID: 28322270
DOI: 10.1038/srep44849

[…] and fastq files were generated., sequencing failed for six track-hd samples, including four premanifest, one manifest and one control subject. quality control analysis was performed using the rna-seqc package, ensuring measures including rrna rate, mapping rate, concordance mapping rate and uniqueness rate were within acceptable ranges. globin depletion was checked by inspecting read […]

PMCID: 5424158
PMID: 28474673
DOI: 10.1038/ncomms15081

[…] rsem v1.2.17 (default parameters). isoform expression levels for each gene were summed to derive the tpm values. quality control assessment of aligned single-cell rna-seq reads was performed using rna-seqc, and the results are summarized in . to remove cells with low-quality sequencing values, four filtering criteria were applied: (1) number of total reads; (2) mapping rate; (3) number […]

PMCID: 5547544
PMID: 28784085
DOI: 10.1186/s12864-017-3967-0

[…] user-provided databases of known exon–intron boundaries. this approach prevents false positive and negative results from probabilistic models. mapping quality control metrics were obtained with rna-seqc v1.1.8 []. read counts were obtained using the standalone script provided by htseq []. the final expression profile was represented by a matrix of read counts, with one row for each gene […]

PMCID: 5694496
PMID: 29184558
DOI: 10.3389/fpls.2017.01905

[…] gene- and transcription-level summaries using htseq-count (anders et al., ). mapped data were subjected to quality control with fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and rna-seqc (deluca et al., ) to ensure sufficient library diversity and transcript coverage, as well as to assess potential contamination with ribosomal rnas. the read counts mapped on the 45,600 cacao […]

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RNA-SeQC in publications

PMCID: 5867863
PMID: 29510583
DOI: 10.3390/genes9030142

[…] keep reads longer than 32 bp with a minimum phred score of 30. alignment of reads to the bovine genome (umd3.1, v84) was accomplished with star v2.5.1b []. following alignment, picard tools [] and rna-seqc [] were used to generate quality control read metrics such as percentage of mapped reads and genomic localization (intronic, intergenic, etc.). uniquely mapped and properly paired reads […]

PMCID: 5811508
PMID: 29440659
DOI: 10.1038/s41467-017-02772-x

[…] of relative mt% only marginally (shifted values < = 0.05) (supplementary fig. )., we have explored if the different tissues show differences in rna-seq quality control metrics obtained with the rna-seqc pipeline. supplementary table  lists the variables used for this analysis. the mapping proportions along the different gene features are shown in supplementary fig.  and . degradation […]

PMCID: 5800601
PMID: 29408885
DOI: 10.1371/journal.pone.0191853

[…] aligner (version 2.3) [] 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 []. read quantification was carried out with featurecounts []. read normalization and differential expression testing were performed with deseq package in r [], and sequence data […]

PMCID: 5796909
PMID: 29434599
DOI: 10.3389/fimmu.2018.00080

[…] was used to calculate normalized fpkm and fpkm confidence intervals for quantification of gene expression (). mapping rates and expression profiling efficiency were calculated using the rseqc and rna-seqc software packages (, ). raw and processed sequencing data are available from gene expression omnibus under the accession gse109182., global visualization of genome-wide cytokine responses […]

PMCID: 5749745
PMID: 29293555
DOI: 10.1371/journal.pone.0190086

[…] long, strand-specific reads per sample. adapterremover was used to trim adapter sequences and the remaining reads were aligned using star to the canfam3 genome. quality control was performed using rna-seqc, to identify samples requiring additional sequencing reads. differential expression was determined using deseq2, which compared sample groups using a likelihood-ratio test (lrt). data […]

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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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