X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=902e806821e6de5ef39eba708edf9d43c82c69ee;hb=810375ef69e0de93188c6fa3819cfc584a32ff34;hp=f6b5ec857f44861c1cd4d5d62b483738e511833d;hpb=4f7502168c3816ba3283385f093e599527e2b144;p=rsem.git diff --git a/README.md b/README.md index f6b5ec8..902e806 100644 --- 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. ## License