Updated boost to v1.55.0

[rsem.git] / README.md

diff --git a/README.md b/README.md
index f6b5ec857f44861c1cd4d5d62b483738e511833d..902e806821e6de5ef39eba708edf9d43c82c69ee 100644 (file)
--- a/README.md
+++ b/README.md
@@ -304,11 +304,14 @@ __N:__ The total number of reads to be simulated. If 'rsem-calculate-expression'
 
 __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;   
@@ -454,9 +457,9 @@ RSEM uses the [Boost C++](http://www.boost.org) and
 [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