README.md is changed

[rsem.git] / README.md

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@@ -51,13 +51,11 @@ variable.
 
 ### Prerequisites
 
 
 ### Prerequisites
 

-C++ and Perl are required to be installed. 
+C++, Perl and R 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.
 
 
 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
 ## <a name="usage"></a> Usage
 
 ### I. Preparing Reference Sequences


@@ -291,17 +289,21 @@ consideration. Because read mapping ambiguity is prevalent among
 isoforms and de novo assembled transcripts, these tools are not ideal
 for DE detection in such conditions. 
 
 isoforms and de novo assembled transcripts, these tools are not ideal
 for DE detection in such conditions. 
 

-**EBSeq**, an empirical Bayesian DE
-analysis tool developed in UW-Madison, can take variance due to read
-mapping ambiguity into consideration by grouping isoforms with parent
-gene's number of isoforms. In addition, it is more robust to
-outliers. RSEM includes the newest version of EBSeq in the folder
-named 'EBSeq'.
-
-For more information about EBSeq (including the paper describing their
-method), please visit <a
+**EBSeq**, an empirical Bayesian DE analysis tool developed in
+UW-Madison, can take variance due to read mapping ambiguity into
+consideration by grouping isoforms with parent gene's number of
+isoforms. In addition, it is more robust to outliers. For more
+information about EBSeq (including the paper describing their method),
+please visit <a

 href="http://www.biostat.wisc.edu/~ningleng/EBSeq_Package">EBSeq
 href="http://www.biostat.wisc.edu/~ningleng/EBSeq_Package">EBSeq

-website</a>. 
+website</a>.
+
+RSEM includes the newest version of EBSeq in its folder
+named 'EBSeq'. To use it, first type
+
+    make ebseq
+
+to compile the EBSeq related codes. 

 
 EBSeq requires gene-isoform relationship for its isoform DE
 detection. However, for de novo assembled transcriptome, it is hard to
 
 EBSeq requires gene-isoform relationship for its isoform DE
 detection. However, for de novo assembled transcriptome, it is hard to