Added error detection for cases such as a read's two mates having different names...

[rsem.git] / README.md

diff --git a/README.md b/README.md
index f6b5ec857f44861c1cd4d5d62b483738e511833d..4184f5d44caf4d94ebb8c5445f25d531517931d8 100644 (file)
--- a/README.md
+++ b/README.md
@@ -56,6 +56,11 @@ To compile EBSeq, which is included in the RSEM package, run
 To install, simply put the rsem directory in your environment's PATH
 variable.
 
 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. 
 ### Prerequisites
 
 C++, Perl and R are required to be installed. 


@@ -209,7 +214,7 @@ Here are some guidance for visualizing transcript coordinate files using IGV:
 
 1) Import the transcript sequences as a genome 
 
 
 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
 
 
 2) Load visualization files
 


@@ -304,11 +309,14 @@ __N:__ The total number of reads to be simulated. If 'rsem-calculate-expression'
 
 __output_name:__ Prefix for all output 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.
 __-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;   
 
 output_name.fa if single-end without quality score;   
 output_name.fq if single-end with quality score;   


@@ -454,9 +462,9 @@ RSEM uses the [Boost C++](http://www.boost.org) and
 [EBSeq](http://www.biostat.wisc.edu/~ningleng/EBSeq_Package/) for
 differential expression analysis.
 
 [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
 
 
 ## <a name="license"></a> License