Fixed a bug in perl scripts for printing error messages

[rsem.git] / README.md

diff --git a/README.md b/README.md
index e85d25001d634b91efb2b9c696474865d5c3ee7d..8d3c15f80f90ed0f52755582af952ebd971b7da4 100644 (file)
--- a/README.md
+++ b/README.md
@@ -158,11 +158,12 @@ plot, run the 'rsem-bam2wig' program on the
 
 Usage:    
 
-    rsem-bam2wig sorted_bam_input wig_output wiggle_name
+    rsem-bam2wig sorted_bam_input wig_output wiggle_name [--no-fractional-weight]
 
-sorted_bam_input: sorted bam file   
-wig_output: output file name, e.g. output.wig   
-wiggle_name: the name the user wants to use for this wiggle plot  
+sorted_bam_input        : Input BAM format file, must be sorted  
+wig_output              : Output wiggle file's name, e.g. output.wig  
+wiggle_name             : the name of this wiggle plot  
+--no-fractional-weight  : If this is set, RSEM will not look for "ZW" tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM. Please note that this option must be at the end of the command line.
 
 #### b) Loading a BAM and/or Wiggle file into the UCSC Genome Browser or Integrative Genomics Viewer(IGV)
 
@@ -298,8 +299,8 @@ named 'EBSeq'.
 
 For more information about EBSeq (including the paper describing their
 method), please visit <a
-href="http://www.biostat.wisc.edu/~ningleng/EBSeq_Package">here</a>. You
-can also find a local version of vignette under
+href="http://www.biostat.wisc.edu/~ningleng/EBSeq_Package">EBSeq
+website</a>. You can also find a local version of vignette under
 'EBSeq/inst/doc/EBSeq_Vignette.pdf'.
 
 EBSeq requires gene-isoform relationship for its isoform DE