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The RNA-seq transcript quantifier with Bias Correction
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INSTALL
LICENSE
NEWS
README
VERSION
build_splice_graph_caller.m
define_segments.m
estimate_ins_size_distr.m
find_overlapping_regions.m
gen_exon_features.m
gen_exon_mask.m
gen_paired_segments.m
gen_segments.m
gen_sequence_features.m
gen_sequence_targets.m
get_adj_bins.m
get_coverage_per_read.m
get_empirical_profiles.m
get_included_thetas.m
get_intron_data.m
get_limits.m
get_paired_data.m
make_release.sh
mean_var_coeff.m
merge_transcripts_by_colocation.m
norm_sequence.m
opt_density.m
opt_profiles_descent.m
opt_seq_descent.m
opt_transcripts_caller.m
opt_transcripts_descent.m
predict_Ridge.m
quad_fun.m
read_density_model.m
rquant.m
rquant_config.sh
rquant_core.m
rquant_rproc.m
run_rquant_alyrata.m
run_rquant_arabidopsis_christina.m
run_rquant_celegans.m
run_rquant_data_sim.m
run_rquant_mip_jonas.m
run_rquant_rgasp.m
sanitise_genes.m
seq_2_kmers.m
setup_rquant.sh
train_Ridge.m
train_norm_sequence.m
write_density_model.m
write_parameters.m
write_rquant_gff3.m

README

----------------------
  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.

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