rsem v1.1.12, add a script to extract transcript-to-gene-map info from Trinity output

[rsem.git] / README.md

diff --git a/README.md b/README.md
index f8c4e2709436f97e446ac3dbbda2306818df70f4..7ef198ce38fbccaa85149267deb89d74ab69f5d3 100644 (file)
--- a/README.md
+++ b/README.md
@@ -13,6 +13,7 @@ Table of Contents
 * [Usage](#usage)
 * [Example](#example)
 * [Simulation](#simulation)
+* [Generate Transcript-to-Gene-Map from Trinity Output](#gen_trinity)
 * [Acknowledgements](#acknowledgements)
 * [License](#license)
 
@@ -187,9 +188,9 @@ The commands for this scenario are as follows:
 
     rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]
 
-estimated_model_file:  File containing model parameters.  Generated by
+estimated_model_file:  file containing model parameters.  Generated by
 rsem-calculate-expression.   
-estimated_isoform_results: File containing isoform expression levels.
+estimated_isoform_results: file containing isoform expression levels.
 Generated by rsem-calculate-expression.   
 theta0: fraction of reads that are "noise" (not derived from a transcript).   
 N: number of reads to simulate.   
@@ -206,6 +207,17 @@ output_name_1.fq & output_name_2.fq if paired-end with quality score.
 
 output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
 
+## <a name="gen_trinity"></a> Generate Transcript-to-Gene-Map from Trinity Output
+
+For Trinity users, RSEM provides a perl script to generate transcript-to-gene-map file from the fasta file produced by Trinity.
+
+### Usage:
+
+    extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
+
+trinity_fasta_file: the fasta file produced by trinity, which contains all transcripts assembled.    
+map_file: transcript-to-gene-map file's name.    
+ 
 ## <a name="acknowledgements"></a> Acknowledgements
 
 RSEM uses the [Boost C++](http://www.boost.org) and