Updated samtools to 0.1.19

[rsem.git] / README.md

diff --git a/README.md b/README.md
index b0fa97cd27c9831e9fb8876f28a5c3d725d6b1fc..e3e890c75196ece8e41ac560df035a0c625981f8 100644 (file)
--- a/README.md
+++ b/README.md
@@ -46,6 +46,13 @@ To compile RSEM, simply run
    
     make
 
+For cygwin users, please uncomment the 3rd and 7th line in
+'sam/Makefile' before you run 'make'.
+
+To compile EBSeq, which is included in the RSEM package, run
+
+    make ebseq
+
 To install, simply put the rsem directory in your environment's PATH
 variable.
 
@@ -111,7 +118,7 @@ using an alternative aligner, you may also want to provide the
 indices are not built.
 
 RSEM requires all alignments of the same read group together. For
-paired-end reads, RSEM also requires the two mates of any alignment be
+vpaired-end reads, RSEM also requires the two mates of any alignment be
 adjacent. To check if your SAM/BAM file satisfy the requirements,
 please run
 
@@ -313,9 +320,9 @@ 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>.
+(including the paper describing their method), please visit [EBSeq's
+website](http://www.biostat.wisc.edu/~ningleng/EBSeq_Package).
+
 
 RSEM includes EBSeq in its folder named 'EBSeq'. To use it, first type
 
@@ -369,7 +376,7 @@ before running either 'EBTest' or 'EBMultiTest'.
 
 Lastly, RSEM provides two scripts, 'rsem-run-ebseq' and
 'rsem-control-fdr', to help users find differential expressed
-genes. First, 'rsem-run-ebseq' calls EBSeq to calculate related statistics
+genes/transcripts. First, 'rsem-run-ebseq' calls EBSeq to calculate related statistics
 for all genes/transcripts. Run 
 
     rsem-run-ebseq --help
@@ -387,6 +394,11 @@ page](http://deweylab.biostat.wisc.edu/rsem/rsem-control-fdr.html). These
 two scripts can perform DE analysis on either 2 conditions or multiple
 conditions.
 
+Please note that 'rsem-run-ebseq' and 'rsem-control-fdr' use EBSeq's
+default parameters. For advanced use of EBSeq or information about how
+EBSeq works, please refer to [EBSeq's
+manual](http://www.bioconductor.org/packages/devel/bioc/vignettes/EBSeq/inst/doc/EBSeq_Vignette.pdf).
+
 Questions related to EBSeq should
 be sent to <a href="mailto:nleng@wisc.edu">Ning Leng</a>.