To install, simply put the rsem directory in your environment's PATH
variable.
+If you prefer to put all RSEM executables to a bin directory, please
+also remember to put 'rsem_perl_utils.pm' and 'WHAT_IS_NEW' to the
+same bin directory. 'rsem_perl_utils.pm' is required for most RSEM's
+perl scripts and 'WHAT_IS_NEW' contains the RSEM version information.
+
### Prerequisites
C++, Perl and R are required to be installed.
1) Import the transcript sequences as a genome
-Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.transcripts.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
+Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.idx.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
2) Load visualization files
__output_name:__ Prefix for all output files.
+__--seed seed:__ Set seed for the random number generator used in simulation. The seed should be a 32-bit unsigned integer.
+
__-q:__ Set it will stop outputting intermediate information.
### Outputs:
output_name.sim.isoforms.results, output_name.sim.genes.results: Expression levels estimated by counting where each simulated read comes from.
+output_name.sim.alleles.results: Allele-specific expression levels estimated by counting where each simulated read comes from.
output_name.fa if single-end without quality score;
output_name.fq if single-end with quality score;
[EBSeq](http://www.biostat.wisc.edu/~ningleng/EBSeq_Package/) for
differential expression analysis.
-We thank earonesty, Dr. Samuel Arvidsson for contributing patches.
+We thank earonesty and Dr. Samuel Arvidsson for contributing patches.
-We thank Han Lin, j.miller for suggesting possible fixes.
+We thank Han Lin, j.miller, Joël Fillon, Dr. Samuel G. Younkin and Malcolm Cook for suggesting possible fixes.
## <a name="license"></a> License