QoRTs pipeline

QoRTs specifications

Information


Unique identifier OMICS_09305
Name QoRTs
Alternative name Quality of RNA-Seq Toolset
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
Computer skills Advanced
Version 1.3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Stephen W. Hartley <>

Publication for Quality of RNA-Seq Toolset

QoRTs IN pipelines

 (4)
2017
PMCID: 5570503
PMID: 28806732
DOI: 10.1371/journal.pgen.1006959

[…] and rs-122-2102). paired end sequencing with a read length of 75 bp was performed on four lanes of illumina hiseq 2500 machines., quality control of sequenced samples was performed using qorts [81] and 7 libraries showing characteristics of rna degradation were excluded from further analysis. sequence was aligned to the grcz10 reference genome with tophat 2.0.13, using a known […]

2017
PMCID: 5690287
PMID: 29144233
DOI: 10.7554/eLife.30860.051

[…] reference genome using tophat (v2.0.13, options: --library-type fr-firststrand, kim et al., 2013). the data were assessed for technical quality (gc-content, insert size, proper-pairs etc.) using qorts (hartley and mullikin, 2015). counts for genes were produced using htseq-count (v0.6.0 options: --stranded=reverse, anders et al., 2015) with the ensembl v85 annotation as a reference. […]

2015
PMCID: 4569390
PMID: 26367423
DOI: 10.1371/journal.pone.0137548

[…] were aligned with the rna-star aligner, using the rn4/rgsc3.4 genome assembly and ensembl transcript annotation, release 69 [52, 53]. quality control metrics were calculated and visualized using the qorts software package, and no major artifacts or abnormalities were found [54]. additional details concerning the sequencing, library preparation, and alignment are described in the si., gene read […]

2015
PMCID: 4569390
PMID: 26367423
DOI: 10.1371/journal.pone.0137548

[…] and no major artifacts or abnormalities were found [54]. additional details concerning the sequencing, library preparation, and alignment are described in the si., gene read counts were provided by qorts, using the same algorithm defined by the htseq package [55]. differential expression analysis was performed using deseq2 [56]. in each analysis, genes with a mean normalized read-pair count […]

QoRTs institution(s)
Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
QoRTs funding source(s)
Supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health.

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