From bbf0a850706b5af654927579105165a5dcb5c4f1 Mon Sep 17 00:00:00 2001 From: Bo Li Date: Wed, 28 Aug 2013 17:11:30 -0500 Subject: [PATCH] Renamed --phred33-quals, --phred64-quals, and --solexa-quals to --bowtie-phred33-quals, --bowtie-phred64-quals, and --bowtie-solex-quals to avoid confusion --- rsem-calculate-expression | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/rsem-calculate-expression b/rsem-calculate-expression index fec2e31..edb6fdd 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, @@ -464,17 +464,17 @@ 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> -- 2.39.2