fixed a bug for transcript set as reference

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 0c900b725107ac55b3074fa6cc0fa5e1b628c978..5acd5937db2f573f9e2a3900baa9bb5b84cdec3c 100644 (file)
--- a/README.md
+++ b/README.md
@@ -40,9 +40,13 @@ variable.
 
 ### Prerequisites
 
+C++ and Perl are required to be installed. 
+
 To take advantage of RSEM's built-in support for the Bowtie alignment
 program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
 
+If you want to plot model learned by RSEM, you should also install R. 
+
 ## <a name="usage"></a> Usage
 
 ### I. Preparing Reference Sequences
@@ -125,21 +129,29 @@ Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/hel
 
 #### c) Visualize the model learned by RSEM
 
-RSEM provides an R script, plotModel.R, for visulazing the model learned.
+RSEM provides an R script, 'rsem-plot-model', for visulazing the model learned.
 
 Usage:
     
-    plotModel.R modelF outF
+    rsem-plot-model modelF outF
 
-modelF: the sample_name.model file generated by RSEM
-outF: the file name for plots generated from the model. It is a pdf file
+modelF: the sample_name.model file generated by RSEM    
+outF: the file name for plots generated from the model. It is a pdf file    
 
 The plots generated depends on read type and user configuration. It
 may include fragment length distribution, mate length distribution,
-read start position distribution (RSPD), quality score vs percentage
-of sequecing error given the reference base, position vs percentage of
-sequencing errro given the reference base.
+read start position distribution (RSPD), quality score vs observed
+quality given a reference base, position vs percentage of sequencing
+error given a reference base.
+
+fragment length distribution and mate length distribution: x-axis is fragment/mate length, y axis is the probability of generating a fragment/mate with the associated length
 
+RSPD: Read Start Position Distribution. x-axis is bin number, y-axis is the probability of each bin. RSPD can be used as an indicator of 3' bias
+
+Quality score vs. observed quality given a reference base: x-axis is Phred quality scores associated with data, y-axis is the "observed quality", Phred quality scores learned by RSEM from the data. Q = -10log_10(P), where Q is Phred quality score and P is the probability of sequencing error for a particular base
+
+Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
+ 
 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will