QoRTs: Quality of RNA-seq Tool-Set

v1.2.25 Revised Sat Mar 4 13:22:59 EST 2017 (Unstable)

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.

• QoRTs vignette. User manual and general how-to. Available as a pdf or on the web.
• Java jar utility help index. The Java utility is responsible for the bulk of the data processing, and contains a number of useful tools. It must be run on all replicates.
• R package help. The R package is responsible for producing visualizations, graphs, plots, and summary tables. (also available as a pdf)
• The Example QC data used in the vignette.
• Documentation for Older versions of QoRTs
• Frequently Asked Questions: Check here if you run into problems!

For advanced users:

• A comprehensive walkthrough of an entire analysis pipeline. This walkthrough primarily covers the analysis and data processing. For more information on the quality control steps see the Vignette, above.
• The example dataset and results for the walkthrough.
• The raw bam files for the example walkthough (File is ~1.1gb).

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 latest version of 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");

Alternatively, the latest STABLE version can be installed using the command:

> install.packages("http://hartleys.github.io/QoRTs/QoRTs_STABLE.tar.gz",
                   repos=NULL, 
                   type="source");

The stable version may lack new features available in the latest version, but has undergone much more testing and is less likely to have problems.

The java jar file does not need to be installed, it can simply be downloaded here and used directly. The latest stable version is available here. 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