X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;fp=README.md;h=8ce3d3897062541a335c291ef9c6dfed89e833f4;hb=613928be32cc58ba330ac30960f4b75440b6d80a;hp=459616fbffb51d04d7582bd5fc1317837b886f1a;hpb=8ca5b7c2fb57bc523431c1e37d5ab9337eccbc37;p=rsem.git
diff --git a/README.md b/README.md
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--- 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.
-
## 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 EBSeq
-website.
+website.
+
+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