"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,
(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>