From: Bo Li <bli@cs.wisc.edu>
Date: Tue, 11 Sep 2012 10:10:36 +0000 (-0500)
Subject: README.md is changed
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=613928be32cc58ba330ac30960f4b75440b6d80a;p=rsem.git

README.md is changed
---

diff --git a/README.md b/README.md
index 459616f..8ce3d38 100644
--- a/README.md
+++ b/README.md
@@ -51,13 +51,11 @@ variable.
 
 ### 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
@@ -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. 
 
-**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
diff --git a/makefile b/makefile
index 3ea1b58..d706f55 100644
--- a/makefile
+++ b/makefile
@@ -1,7 +1,7 @@
 CC = g++
 CFLAGS = -Wall -c -I.
 COFLAGS = -Wall -O3 -ffast-math -c -I.
-PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads ebseq
+PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 
 all : $(PROGRAMS)