Quality of RNA-seq Toolset
v0.3.26 Revised Fri Nov 6 15:14:14 EST 2015
The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets. Its primary function is to aid in the detection and identification of errors, biases, and artifacts produced by paired-end high-throughput RNA-Seq technology. In addition, it can produce count data designed for use with differential expression and differential exon usage tools, as well as individual-sample and/or group-summary genome track files suitable for use with the UCSC genome browser (or any compatible browser).
The entire QoRTs toolkit can be used in almost any operating system that supports java and R.
The most recent release of QoRTs is available on the QoRTs github page. Additional help and documentation is available online here. The creator and maintainer of QoRTs can be reached by emailing "QoRTs-contact" (at) list.nih.gov.
If you use QoRTs and find it helpful, you can cite it in your publications as:
Hartley SW, Mullikin JC. QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. BMC Bioinformatics. doi: 10.1186/s12859-015-0670-5
The R package can be installed in R using the command:
> install.packages("http://hartleys.github.io/QoRTs/QoRTs_LATEST.tar.gz",
repos=NULL,
type="source");
The java jar file does not need to be installed, it can simply be downloaded and used directly. Just execute it using the java command:
java -jar /path/to/jarfile/QoRTs.jar QC input.bam anno.gtf.gz /output/dir/
See the FAQ if you have trouble installing QoRTs.
The example QC output used in the vignette can be found on the github main page, and installed with the command:
install.packages("http://hartleys.github.io/QoRTs/QoRTsExampleData_LATEST.tar.gz",
repos = NULL,
type="source")
The original bam files are too large to upload to github. These files can be found here. (File is ~1.5gb)
There is also a comprehensive walkthrough of the entire analysis pipeline, run on a different example dataset with example bam files.
Additional options and syntax information for the main QC java utility can be found using the command:
java -jar /path/to/jarfile/QoRTs.jar QC --man
Options and information about other sub-utilities within the java package can be found using the command:
java -jar /path/to/jarfile/QoRTs.jar --man
And for each sub-utility:
java -jar /path/to/jarfile/QoRTs.jar utilname --man
For help with individual R functions in the R utility, use the R command:
> help(functionname);
For a full listing of all help topics for the R utility, use the R command:
> help(package="QoRTs");
This software is "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus QoRT Package User Manual cannot be copyrighted. This software is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use.
Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose.
In any work or product derived from this material, proper attribution of the authors as the source of the software or data should be made, using "NHGRI Genome Technology Branch" as the citation.
NOTE: The scala package includes (internally) the sam-JDK library (sam-1.113.jar), from picard tools, which is covered under the MIT license. The MIT license and copyright information can be accessed using the command: java -jar /path/to/jarfile/QoRTs.jar --man samjdkinfo