File	Date	Author	Commit
doc	2013-05-17	Ian Reid	[55d807] Added doc/Program_command_lines.txt
example_data	2013-05-17	Ian Reid	[10b29d] Updated Tutorial.txt and added README
lib	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
test	2013-03-12	Ian Reid	[9401ec] Started doc/Tutorial.txt
LICENSE	2013-04-17	Ian Reid	[5b50b6] Added license and copyright notices
README	2013-05-17	Ian Reid	[10b29d] Updated Tutorial.txt and added README
SAM2origin.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
__init__.py	2013-03-10	ian	[bb8b2e] Initial commit
accumulateFragmentationProbabilityProfilesForSelectedTranscripts.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
calcTranscriptFragmentationProbabilities.py	2013-05-17	Ian Reid	[10b29d] Updated Tutorial.txt and added README
compareMaps.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
countErrorsAndQualityScores.py	2013-05-17	Ian Reid	[55d807] Added doc/Program_command_lines.txt
get_isoforms_from_coverage.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
get_transcript_coverage_counts.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
get_transcript_origin_counts.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
postprocess_simulation.sh	2013-04-19	Ian Reid	[821e2c] Corrected simulated reads file path
simulateRNA_Seq.py	2013-05-17	Ian Reid	[10b29d] Updated Tutorial.txt and added README
trimSAMbyRead.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'
truncateSAM.py	2013-05-16	Ian Reid	[26ed90] Merge remote-tracking branch 'origin/master'

Read Me

RNA-Seq-Simulator is a suite of Python programs for realistic simulation of the short reads from Illumina RNA-Seq
experiments. It was developed at the Centre for Structural and Functional Genomics of Concordia University and is
released under a FreeBSD license.

Installation

Decompress the download package in any convenient location.

To use the programs you will need to have the following programs installed on your PATH:
python (2.7 or later) with packages biopython (1.60 or later),pysam, numpy (available from https://pypi.python.org/pypi)
bedtools (available from http://code.google.com/p/bedtools)
bam2fastq (available from www.hudsonalpha.org/gsl/information/software/bam2fastq‎)
samtools (available from http://sourceforge.net/projects/samtools/files/samtools/)
bgzip and tabix (available from http://sourceforge.net/projects/samtools/files/tabix/)

Usage

See doc/Tutorial.txt for a usage example.