Does bowtie need to have reads in the standard sanger format or can it accept the default file created from the 1.4 illumina pipeline in which the quals are not standard sanger?
Cheers
L
Cheers
L
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man ascii
#!/usr/bin/env perl ################################################ # prints a table with phred, ASCII, phred+33, phred+64, p ################################################ use strict; use warnings; my @phreds = (0..62); my $step = 2; printf "%6s %6s %6s %6s %10s\n", 'phred', 'ASCII', 'Ill33', 'Ill64', 'p'; for (my $i = 0; $i < @phreds; $i+=$step ){ my $phred = $phreds[$i]; printf "%6d %6d %6s %6s %10f\n", $phred, $phred+64, chr($phred+33), chr($phred+64), phred2p($phred); } sub phred2p{ return 10 ** (-(shift) / 10.0 ); }
--phred64-quals input quals are Phred+64 (same as --solexa1.3-quals)
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