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SimReg --------------------- A Simulated Regression based algorithm for transcriptome quantification. REQUIREMENTS --------------------------- 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 )
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