Updated samtools to 0.1.19

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index edb6fddf5458d3d80da38dc9996d586e902a8b9d..3f2817d083fac4605cbcb0ded7baaa6e6900db99 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -354,14 +354,10 @@ rsem-calculate-expression
 
 =head1 SYNOPSIS
 
-=over
-
- rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
- rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
+ rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name 
+ rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name 
  rsem-calculate-expression [options] --sam/--bam [--paired-end] input reference_name sample_name
 
-=back
-
 =head1 ARGUMENTS
 
 =over
@@ -528,6 +524,10 @@ Suppress the output of logging information. (Default: off)
 
 Show help information.
 
+=item B<--version>
+
+Show version information.
+
 =back
 
 =head1 DESCRIPTION
@@ -718,7 +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 \