X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-calculate-expression;h=3f2817d083fac4605cbcb0ded7baaa6e6900db99;hb=58d504aaf36ae486b1dba6d03e0e9f1c25855037;hp=62339cb4aa41b1e43a5da611a8bb110f018cf399;hpb=80182d3120cde6e3831fc3ea99af91f20dade08b;p=rsem.git

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 62339cb..3f2817d 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -524,6 +524,10 @@ Suppress the output of logging information. (Default: off)
 
 Show help information.
 
+=item B<--version>
+
+Show version information.
+
 =back
 
 =head1 DESCRIPTION
@@ -714,7 +718,7 @@ Assume the path to the bowtie executables is in the user's PATH environment vari
                            /ref/mouse_125 \
                            mmliver_single_without_quals
 
-4) Data are the same as 1). We want to take a fragment length distribution into consideration. We set the fragment length mean to 150 and the standard deviation to 35. In addition to a BAM file, we also want to generate credibility intervals.  We allow RSEM to use 1GB of memory for CI calculation:
+4) Data are the same as 1). This time we assume the bowtie executables are under '/sw/bowtie'. We want to take a fragment length distribution into consideration. We set the fragment length mean to 150 and the standard deviation to 35. In addition to a BAM file, we also want to generate credibility intervals.  We allow RSEM to use 1GB of memory for CI calculation:
 
  rsem-calculate-expression --bowtie-path /sw/bowtie \
                            --phred64-quals \