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Bioinformatics Research Technology Platform

Homer

Displaying Seqlogoss correctly

The '-bits' option only works for de-novo motifs. There are two bugs that need to be corrected so that bits works for known motifs

findKnownMotifs.pl

Line 232 & 233: Remove the -S option

'seqlogo -a $bits -f "$tmpFile" -F PNG -S -c -o "$directory/$knownDir/$logoFile" -h $height 
     -w $width';
'seqlogo -a $bits -f "$tmpFile" -F PDF -S -c -o "$directory/$knownDir/$logoFile" -h $height 
     -w $width 2> /dev/null';

should read

'seqlogo -a $bits -f "$tmpFile" -F PNG -c -o "$directory/$knownDir/$logoFile" -h $height -w $width';
'seqlogo -a $bits -f "$tmpFile" -F PDF -c -o "$directory/$knownDir/$logoFile" -h $height -w $width 2> /dev/null';

findMotifsGenome.pl

Lines 934 & 935

my $options = $cmd->{'bits'};
$options = " -optimize" if ($floatAction eq 'OPTPVALUE');

should read

my $options = " ".$cmd->{'bits'};
$options .= " -optimize" if ($floatAction eq 'OPTPVALUE');

ie leading space before "-bits", and ensure the -optimize is concatenated