RNA-SeQC protocols

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 No



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Publication for RNA-SeQC

RNA-SeQC IN pipelines

PMCID: 5424158
PMID: 28474673
DOI: 10.1038/ncomms15081

[…] rsem v1.2.17 (default parameters)56. 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-seqc57, and the results are summarized in supplementary data 3. to remove cells with low-quality sequencing values, four filtering criteria were applied: (1) number of total reads; (2) mapping […]

PMCID: 5557398
PMID: 28806978
DOI: 10.1186/s13045-017-0515-y

[…] sequence reads were trimmed using cutadapt 1.2.1 [20] and mapped to the human 1000 genomes build 37 (grch37) using tophat 2 (2.0.4) [21]. quality control of rna sequencing data was performed with rna-seqc [22] (additional file 1: table s2). detailed information of rna sequencing and computational analysis is provided in additional file 2., fusion genes were detected using a two-pronged […]

PMCID: 4768675
PMID: 26925311
DOI: 10.7717/peerj.1616

[…] 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 […]

PMCID: 5099203
PMID: 26857698
DOI: 10.1136/annrheumdis-2015-208659

[…] 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: 4660214
PMID: 26573325
DOI: 10.1038/ncomms9891

[…] files were processed using picard tools v1.54 (http://picard.sourceforge.net/), and the final bam files indexed using samtools index v0.1.11 (ref. 35). rna-seq run quality was assessed using the rna-seqc package36 using the same gencode 16.gtf file and hg19 reference as was used to create the index. transcript quantification was performed using cufflinks16 v2.02 running in quantification […]

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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