X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-calculate-expression;h=3f2817d083fac4605cbcb0ded7baaa6e6900db99;hb=6306c61d30a4e727027c26488272c9ff683f8236;hp=fec2e310471c331d4bdf3b745ad4c129f2f5aee1;hpb=f0aa264bd96a2e742cfe186767db69270b896899;p=rsem.git

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index fec2e31..3f2817d 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -88,9 +88,9 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
 	   "bowtie-e=i" => \$E,
 	   "bowtie-m=i" => \$maxHits,
 	   "bowtie-chunkmbs=i" => \$chunkMbs,
-	   "phred33-quals" => \$phred33,
-	   "phred64-quals" => \$phred64, #solexa1.3-quals" => \$phred64,
-	   "solexa-quals" => \$solexa,
+	   "bowtie-phred33-quals" => \$phred33,
+	   "bowtie-phred64-quals" => \$phred64, #solexa1.3-quals" => \$phred64,
+	   "bowtie-solexa-quals" => \$solexa,
 	   "forward-prob=f" => \$probF,
 	   "fragment-length-min=i" => \$minL,
 	   "fragment-length-max=i" => \$maxL,
@@ -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
@@ -464,17 +460,17 @@ The path to the bowtie executables. (Default: the path to the bowtie executables
 
 (Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use bowtie's default)
 
-=item B<--phred33-quals>
+=item B<--bowtie-phred33-quals>
 
-Input quality scores are encoded as Phred+33. (Default: on)
+(Bowtie parameter) Input quality scores are encoded as Phred+33. (Default: on)
 
-=item B<--phred64-quals>
+=item B<--bowtie-phred64-quals>
 
-Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. >= 1.3). (Default: off)
+(Bowtie parameter) Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. >= 1.3). (Default: off)
 
-=item B<--solexa-quals>
+=item B<--bowtie-solexa-quals>
 
-Input quality scores are solexa encoded (from GA Pipeline ver. < 1.3). (Default: off)
+(Bowtie parameter) Input quality scores are solexa encoded (from GA Pipeline ver. < 1.3). (Default: off)
 
 =item B<--forward-prob> <double>
 
@@ -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 \