X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=README.md;h=8d3c15f80f90ed0f52755582af952ebd971b7da4;hp=ed5acc050230fd50a1803e31d24790a8919ce8fd;hb=1b2999c4407ef8419fb89b66b843b7141caff4da;hpb=6eec553ba4ab1cb1c6f48cd14d9e5c92c7d85798

diff --git a/README.md b/README.md
index ed5acc0..8d3c15f 100644
--- 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)