Where are .motif files from homer knownResults?

Question

[Benn]

I also asked this question on SE bioinformatics, but since I didn't get any answers yet, I would like to ask it here as well. Hope you don't mind.

I have been using homer's findMotifsGenome.pl, but with my new version (v4.9.1) of homer I don't get .motif files in the knownResults folder. I do get them in the homerResults (de novo) folder, though. With my previous version of homer I did get them and used them to find which peaks are in which motif. Which is what I would like to do

Does anyone know why there are no .motif files? I have only .svg files. I have seen that for the homerResults the .motif files are concatenated already into a file called homerMotifs.all.motifs, but no such file for knownResults.

Does anyone know of this 'bug' in the new version of homer? Any solutions?

My code:

findMotifsGenome.pl All_peaks.txt Homo_sapiens.GRCh38.dna.primary_assembly.fa Peaks.All -p 20

Answer 1

[Malcolm.Cook]

If you edit the file findKnownMotifs.pl and move the call to printMotif to come before testing $svgFlag you will find that .motif files are printed again.

In the following I have commented out the call from where it need not be, and introduced it as the first line, right before the if block:

   printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                                        
    if ($svgFlag) {
        my $str = HomerSVGLogo::motif2svg($_,$bitFlag,$rnaFlag2);
            open SVG, ">$directory/$knownDir/$logoFile.svg";
            print SVG $str;
            close SVG;
            print MAIN "$str\n";
    } else {
    #printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                               
            `profile2seq.pl "$directory/$knownDir/$matrixFile" 100 > "$tmpFile"`;
            my $width = $widthFactor * $_->{'len'};
            `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 $width 2> /dev/null`;
    print MAIN "<IMG src=\"$knownDir/$logoFile.png\"/>";
}

I expect this change was mistakenly introduced while refactoring the code to support svg as alternate output format for logos.

I have reported this to the author of this code.

~ Similarly afflicted in Kansas USA!

[Benn]

Wow, thanks for your hacking solution man. I didn't expect any solution anymore, I thought it was just me. So when my co-workers asked again for the motifs last week, I found out that you can also use the old method in homer (without the svg). You'll have to include -seqlogo to the findMotifsGenome.pl command. You'll have to install some other stuff first, though. Sorry didn't have time to post it here yet (I am not very active here anymore).