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The RNA-seq transcript quantifier with Bias Correction
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---------------------- rQuant version 2.1 ---------------------- DESCRIPTION rQuant is a programme to determine abundances of multiple transcripts per gene locus from RNA-Seq measurements. It can simultaneously estimate the effect of biases introduced by experimental settings. REQUIREMENTS - Octave or Matlab - Python >=2.6.5 and Scipy >=0.7.1 - SAMTools >= 0.1.7 GETTING STARTED To install rQuant and the required software please follow the instructions in INSTALL in this directory. CONTENTS All relevant scripts for rQuant are located in the subdirectory src. rquant.sh is the main script to start rQuant. In the same subdirectory you find the script read_stats.sh that generates a statistic about the read alignments and the covered genes. GALAXY rQuant can be used as a web service embedded in a Galaxy instance (cf. http://galaxy.fml.tuebingen.mpg.de/tool_runner?tool_id=rquantweb). The Galaxy tool configuration file of rQuant is located in the subdirectory galaxy along with XML file for loading example data and instructions (rquant_web.xml and rquant_web_instructions.xml, respectively). Please adapt the paths to the respective tools in command section of the XML files as indicated. The subdirectory test_data contains all data for running a functional test in Galaxy (e.g. with sh run_functional_test.sh -id rquantweb). You may need to move these test files into the Galaxy test-data directory. DOCUMENTATION More information is available in doc/rquant_web_instructions.txt, doc/rquant_web.txt, and doc/read_stats.txt. Examples for running rQuant can be found in examples/./run_example.sh. You can also find information on rQuant.web and rQuant on http://fml.mpg.de/raetsch/suppl/rquant/web and http://fml.mpg.de/raetsch/suppl/rquant, respectively. LICENSE rQuant is licensed under the GPL version 3 or any later version (cf. LICENSE). CITE US If you use rQuant in your research you are kindly asked to cite the following publications: * Regina Bohnert and Gunnar Raetsch: rQuant.web: A tool for RNA-Seq-based transcript quantitation. Nucleic Acids Research, 38(Suppl 2):W348-51, July 2010. * Regina Bohnert, Jonas Behr, and Gunnar Raetsch: Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10(S13):P5, October 2009.