SimReg
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A Simulated Regression based algorithm for transcriptome quantification. 


REQUIREMENTS
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SimReg is a standalone tool that requires gcc 4.0 or greater, and runs on Linux.  

It depends on:

1. Boost (http://www.boost.org) version 1.38 or higher, 

2. CVXOPT: A Python Package for Convex Optimization: http://openopt.org/CVXOPT

3. TCLAP library: http://sourceforge.net/projects/tclap/


To run SimReg simply use the following command: $PWD/run-mcreg.sh
(always use absolute path for run-mcreg.sh)

First you will need to compile all source files using the make command.
(The C++ source files have been compiled on Ubuntu server so the program may work as is)

Usually the transcriptome alignment is done with the following command:
bowtie --best -v 3 -k 60 -p 12 --chunkmbs 128 [PathToBowtieIndexes] -f -1 [pair1.fa] -2 [pair2.fa] -I [intValue] -X [intValue] -S $PWD/bowtie_k60v0best.sam > bowtie.log
(see Bowtie manual for more info about the flags: http://bowtie-bio.sourceforge.net/manual.shtml )