File	Date	Author	Commit
docs	2013-06-04	Ian Reid	[7048d3] Synchronized documentation with revised command...
example_data	2013-05-27	Ian Reid	[f4f13b] Updated Using_Tuque.txt
lib	2013-08-23	Ian Reid	[6b54b5] Corrected bug in tuqueSplice that prevented use...
LICENSE	2013-04-09	Ian Reid	[d485d6] Added license and started documentation
README	2013-08-23	Ian Reid	[8211d3] Bumped version to 1.0.4
tuque.cfg.template	2013-06-04	Ian Reid	[7048d3] Synchronized documentation with revised command...
tuqueCount	2013-04-15	Ian Reid	[9da3e1] Made stderr redirection syntax in tuqueSplice m...
tuqueIndex	2013-06-04	Ian Reid	[7048d3] Synchronized documentation with revised command...
tuqueMap	2013-08-23	Ian Reid	[6b54b5] Corrected bug in tuqueSplice that prevented use...
tuqueSplice	2013-08-23	Ian Reid	[6b54b5] Corrected bug in tuqueSplice that prevented use...
tuqueSplice_ps	2013-06-04	Ian Reid	[7048d3] Synchronized documentation with revised command...

Read Me

Tuque version 1.0.4

Tools for mapping RNA-Seq reads to eukaryotic genomes.

Tuque depends on other open-source software. Before using any of the Tuque programs,
ensure that these programs are available on your system:
A Unix operating system, with bash, sort, awk, and grep
Python 2.7 or newer     - Available from http://www.python.org/ . Don't use Python 3.
Biopython               - Available from http://biopython.org/wiki/Download
bowtie and bowtie-build - Available from http://bowtie-bio.sourceforge.net/index.shtml . Don't use Bowtie 2.
blat and pslCDnaFilter  - Available from http://hgdownload.cse.ucsc.edu/admin/exe/
samtools and tabix      - Available from http://sourceforge.net/projects/samtools/files/
genomeCoverageBed       - Available from http://code.google.com/p/bedtools/

The programs can be installed anywhere; they do not need to be in a system directory or on the PATH.

To install Tuque, download and decompress http://sourceforge.net/projects/tuque/files/tuque.v1.0.4.tar.gz
In the resulting tuque folder, edit the file tuque.cfg.template so that the program paths correspond to the
locations on your system and save it as tuque.cfg.

Instructions for using the programs are available in the docs subfolder of the distribution package. You can
test your installation with the small data set in example_data.