QoRTs statistics

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Protocols

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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Versioning


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Documentation


Maintainer


  • person_outline Stephen W. Hartley

Publication for Quality of RNA-Seq Toolset

QoRTs citations

 (10)
library_books

SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program

2018
eLife
PMCID: 5963917
PMID: 29741478
DOI: 10.7554/eLife.37419.041

[…] ionSeq.Data for SRSF3 iCLIP was filtered for sites that also appeared in the GFP iCLIP control, then converted to bed format. This data was then merged with the exon/junction feature annotations from QoRTS (including de novo junction calls) using BedTools. Detained intron data () was similarly merged with the QoRTS annotation. For k-means clustering of time-point data, a minimum autocorrelation fi […]

call_split

Loss of the chromatin modifier Kdm2aa causes BrafV600E independent spontaneous melanoma in zebrafish

2017
PLoS Genet
PMCID: 5570503
PMID: 28806732
DOI: 10.1371/journal.pgen.1006959
call_split See protocol

[…] Quality control of sequenced samples was performed using QoRTs [] 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 transcrip […]

library_books

Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

2017
Genome Med
PMCID: 5518101
PMID: 28724449
DOI: 10.1186/s13073-017-0452-y

[…] e per each BAM given as input. The assemblies were then merged into a master transcriptome via the cuffmerge tool. We then computed the detection and visualization of exons and splice junctions using QoRTs v1.0.1 [] (java -Xmx4G -jar < QORTS_JARFILE > QC --stranded command) and JunctionSeq v0.6.9 [] software (runJunctionSeqAnalyses function with analysis.type = exonsOnly and method.GLM = advanced […]

call_split

Reciprocal regulation of the Il9 locus by counteracting activities of transcription factors IRF1 and IRF4

2017
Nat Commun
PMCID: 5437292
PMID: 28497800
DOI: 10.1038/ncomms15366
call_split See protocol

[…] ina standard protocol. Quality control on the sequencing data was performed with the FastQC tool (available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), as well as the comprehensive Qorts suite. Inspecting the produced reports, all samples were deemed of good quality for further processing. Short reads alignment was performed with the ENSEMBL Mus_musculus.GRCm38 chosen as the ref […]

library_books

The co existence of transcriptional activator and transcriptional repressor MEF2 complexes influences tumor aggressiveness

2017
PLoS Genet
PMCID: 5413110
PMID: 28419090
DOI: 10.1371/journal.pgen.1006752

[…] Technology).RNA-sequencing libraries were prepared as previously described [] and sequenced on a Illumina HiSeq 1000 apparatus (Illumina) to a depth of 50–80 million paired-end reads per sample. The QoRts package was used to evaluate data quality and STAR2.5.2a for reads mapping to the GRCh37.74 genome assembly. RSEM was used for quantifying gene and isoform abundances []. Here we provide the lis […]

library_books

A high resolution mRNA expression time course of embryonic development in zebrafish

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

[…] ligned to the GRCz10 reference genome using TopHat (v2.0.13, options: --library-type fr-firststrand, ). The data were assessed for technical quality (GC-content, insert size, proper-pairs etc.) using QoRTs (). Counts for genes were produced using htseq-count (v0.6.0 options: --stranded=reverse, ) with the Ensembl v85 annotation as a reference. The processed count data are in . […]

Citations

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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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