text: user939: 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.
  PS. I tried to call Chuck for help, but he was not answering his phone...
  PS2. I will ask this question on Biostars to hopefully get more response than here.
  
  user48: The relevant help page of homer seems to be this one.
  On section 13 it says:
  
  An HTML page is created in the output directory named homerResults.html along with a directory named "homerResults/" that contains all of the image and other support files to create the page.  These pages are explicitly created by running a subprogram called "compareMotifs.pl".
  
  You seeem to have this images on the expected folder.
  Also on section 12 it says:
  
  They [The *.motifs files] are reported in the output directories from findMotifs.pl and findMotifsGenome.pl
  
  So you'll need to specify the output directory for findMotifsGenome.pl.
  
  user1692: I have provided a solution in Biostars:
  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.
  
original_text: 939: <p>I have been using homer's <code>findMotifsGenome.pl</code>, but with my new version (v4.9.1) of <code>homer</code> I don't get <code>.motif</code> files in the <code>knownResults</code> folder. I do get them in the <code>homerResults</code> (<em>de novo</em>) folder, though. With my previous version of <code>homer</code> I did get them and used them to find which peaks are in which motif. Which is what I would like to do</p>
  
  <p>Does anyone know why there are no <code>.motif</code> files? I have only <code>.svg</code> files. I have seen that for the <code>homerResults</code> the <code>.motif</code> files are concatenated already into a file called <code>homerMotifs.all.motifs</code>, but no such file for <code>knownResults</code>.</p>
  
  <p>PS. I tried to call Chuck for help, but he was not answering his phone...</p>
  
  <p>PS2. I will ask this question on Biostars to hopefully get more response than here.</p>
   48: <p>The relevant help page of homer seems to be this <a href="http://homer.ucsd.edu/homer/motif/index.html" rel="nofollow noreferrer">one</a>.</p>
  
  <p>On section 13 it says:</p>
  
  <blockquote>
    <p>An HTML page is created in the output directory named homerResults.html along with a directory named "homerResults/" that contains all of the image and other support files to create the page.  These pages are explicitly created by running a subprogram called "compareMotifs.pl".</p>
  </blockquote>
  
  <p>You seeem to have this images on the expected folder.<br>
  Also on section 12 it says:</p>
  
  <blockquote>
    <p>They [The *.motifs files] are reported in the output directories from findMotifs.pl and findMotifsGenome.pl</p>
  </blockquote>
  
  <p>So you'll need to specify the output directory for findMotifsGenome.pl.</p>
   1692: <p>I have provided a <a href="https://www.biostars.org/p/269966/#280121" rel="nofollow noreferrer">solution</a> in Biostars:</p>
  
  <p>If you edit the file <code>findKnownMotifs.pl</code> and move the call to <code>printMotif</code> to come before testing <code>$svgFlag</code> you will find that <code>.motif</code> files are printed again. </p>
  
  <p>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 <code>if</code> block:</p>
  
  <pre><code>   printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                                        
      if ($svgFlag) {
          my $str = HomerSVGLogo::motif2svg($_,$bitFlag,$rnaFlag2);
              open SVG, "&gt;$directory/$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 &gt; "$tmpFile"`;
              my $width = $widthFactor * $_-&gt;{'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 $width 2&gt; /dev/null`;
    print MAIN "&lt;IMG src=\"$knownDir/$logoFile.png\"/&gt;";
  }
  </code></pre>
  
  <p>I expect this change was mistakenly introduced while refactoring the code to support svg as alternate output format for logos.</p>
  
  <p>I have reported this to the author of this code.</p>
  