Enable RSEM to visualize the model learned from data

[rsem.git] / README.md

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 Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
 
+#### c) Visualize the model learned by RSEM
+
+RSEM provides an R script, plotModel.R, for visulazing the model learned.
+
+Usage:
+    
+    plotModel.R 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
+
+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.
+
 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will