From: Bo Li Date: Sat, 11 Jan 2014 20:17:32 +0000 (-0600) Subject: Removed unnecessary spaces in POD doc of rsem-calculate-expression' X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=5a1c0c7e480ffda84f83d224246c754a4761500f Removed unnecessary spaces in POD doc of rsem-calculate-expression' --- diff --git a/rsem-calculate-expression b/rsem-calculate-expression index 3f2817d..c157f54 100755 --- a/rsem-calculate-expression +++ b/rsem-calculate-expression @@ -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). 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: +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 \ @@ -732,7 +732,7 @@ Assume the path to the bowtie executables is in the user's PATH environment vari /ref/mouse_125 \ mmliver_single_quals -5) '/data/mmliver_paired_end_quals.bam', paired-end reads with quality scores. We want to use 8 threads: +5) '/data/mmliver_paired_end_quals.bam', paired-end reads with quality scores. We want to use 8 threads: rsem-calculate-expression --paired-end \ --bam \