X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fbowtie_seq;h=07374216593d0a6f24d7fd858f6de3b21c6377ec;hb=72bdee400078921c708370e9b9e101df4c5ebbe1;hp=19368f84452db6ffb3def6777d1ac646e64c9d1e;hpb=25a6b40e414b3a6465f18239f37a980d77d6e062;p=biopieces.git

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 19368f8..0737421 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -103,7 +103,7 @@ push @args, "-n $options->{ 'mismatches' }";
 push @args, "-v $options->{ 'mismatches' }";  # DANGER: using seed mismatches as alignment mismatches - may work, may not!
 push @args, "-f" if $type eq "FASTA";
 push @args, "-p $options->{ 'cpus' }";
-push @args, "--phred64-quals" unless $type eq "FASTA";
+push @args, "--phred33-quals" unless $type eq "FASTA";
 
 if ( defined $options->{ 'max_hits' } ) {
     push @args, "-k $options->{ 'max_hits' }";