### 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.
-If you want to plot model learned by RSEM, you should also install R.
-
## <a name="usage"></a> Usage
### I. Preparing Reference Sequences
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
-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