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RNA-Seq-Simulator.v1.0.tar.gz 2013-05-17 9.8 MB
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README 2013-05-17 913 Bytes
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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.
Source: README, updated 2013-05-17