text: user180: I am trying to a recently published software called diffTF and contacted the authors on how to obtain the input HOCOMOCO files for GRCh38. While I wait for the answer, I thought I would post the question here as well:
  The tool requires bed files for each of the transcription factors (TF) in the genome, such as this bed file (TAB separated), which seems to give the locations of different TF binding sites in the genome:
  chr1    3457132     3457141     GTTGCGTGA   1266   +
  chr1    4595374     4595383     GTTGCGTGA   1266   -
  chr1    4996631     4996640     TTTGCGTGC   1276   +
  chr1    5005357     5005366     TTTGCGTGC   1276   +
  chr1    5170456     5170465     TTTGCGTGC   1276   -
  chr1    5567302     5567311     GTTGCGTGA   1266   -
  chr1    8676279     8676288     TTTGCGTGC   1276   -
  chr1    8859719     8859728     GTTGCGTGA   1266   +
  chr1    9600920     9600929     GTTGCGTGA   1266   +
  chr1    9650971     9650980     GTTGCGTGA   1266   +
  ...
  
  Then there is a symbols file to map the TF to their gene(?) that looks like this:
  SYMBOL  ENSEMBL HOCOID
  Ahr     ENSMUSG00000019256      AHR
  Aire    ENSMUSG00000000731      AIRE
  Alx1    ENSMUSG00000036602      ALX1
  Ar      ENSMUSG00000046532      ANDR
  Tfap2a  ENSMUSG00000021359      AP2A
  Tfap2b  ENSMUSG00000025927      AP2B
  Tfap2c  ENSMUSG00000028640      AP2C
  Tfap2d  ENSMUSG00000042596      AP2D
  
  I googled for HOCOMOCO and found a bunch of pwn or words files, but none of them seems to be similar to the bed file above. Any ideas where to get these for GRCh38?
  
  user4190: I guess you're right that you need predictions of transcription factor binding site (TFBS) through genome.
  There're two options to get them: 
  
  You can generate predictions using any motif scanning tool. E.g. you can use our tool SPRY-SARUS which is able to generate bed-file in necessary format.
  In this case, you can choose more or less strict thresholds for each prediction (i.e. more false positives vs more false negatives). Standard thresholds for HOCOMOCO motifs can be found at its downloads page (we, as HOCOMOCO authors, recommend thresholds corresponding to P-value of 0.0005).
  I had no experience with diffTF but it seems that authors prepared TFBS predictions and put them on their site. Please, take a look at this page of manual. If you don't need extra-flexibility in the generation of TFBS predictions, it can be the simplest way to proceed.
  
  
original_text: 180: <p>I am trying to a recently published software called diffTF and contacted the authors on how to obtain the input <a href="http://hocomoco11.autosome.ru/" rel="nofollow noreferrer">HOCOMOCO</a> files for GRCh38. While I wait for the answer, I thought I would post the question here as well:</p>
  
  <p>The tool requires bed files for each of the transcription factors (TF) in the genome, such as this bed file (TAB separated), which seems to give the locations of different TF binding sites in the genome:</p>
  
  <pre><code>chr1    3457132     3457141     GTTGCGTGA   1266   +
  chr1    4595374     4595383     GTTGCGTGA   1266   -
  chr1    4996631     4996640     TTTGCGTGC   1276   +
  chr1    5005357     5005366     TTTGCGTGC   1276   +
  chr1    5170456     5170465     TTTGCGTGC   1276   -
  chr1    5567302     5567311     GTTGCGTGA   1266   -
  chr1    8676279     8676288     TTTGCGTGC   1276   -
  chr1    8859719     8859728     GTTGCGTGA   1266   +
  chr1    9600920     9600929     GTTGCGTGA   1266   +
  chr1    9650971     9650980     GTTGCGTGA   1266   +
  ...
  </code></pre>
  
  <p>Then there is a symbols file to map the TF to their gene(?) that looks like this:</p>
  
  <pre><code>SYMBOL  ENSEMBL HOCOID
  Ahr     ENSMUSG00000019256      AHR
  Aire    ENSMUSG00000000731      AIRE
  Alx1    ENSMUSG00000036602      ALX1
  Ar      ENSMUSG00000046532      ANDR
  Tfap2a  ENSMUSG00000021359      AP2A
  Tfap2b  ENSMUSG00000025927      AP2B
  Tfap2c  ENSMUSG00000028640      AP2C
  Tfap2d  ENSMUSG00000042596      AP2D
  </code></pre>
  
  <p>I googled for HOCOMOCO and found a bunch of pwn or words files, but none of them seems to be similar to the bed file above. Any ideas where to get these for GRCh38?</p>
   4190: <p>I guess you're right that you need predictions of transcription factor binding site (TFBS) through genome.
  There're two options to get them: </p>
  
  <ol>
  <li>You can generate predictions using any motif scanning tool. E.g. you can use our tool <a href="https://github.com/VorontsovIE/sarus" rel="nofollow noreferrer">SPRY-SARUS</a> which is able to generate bed-file in necessary format.
  In this case, you can choose more or less strict thresholds for each prediction (i.e. more false positives vs more false negatives). Standard thresholds for HOCOMOCO motifs can be found at its downloads <a href="http://hocomoco11.autosome.ru/downloads_v11" rel="nofollow noreferrer">page</a> (we, as HOCOMOCO authors, recommend thresholds corresponding to P-value of 0.0005).</li>
  <li>I had no experience with diffTF but it seems that authors prepared TFBS predictions and put them on their site. Please, take a look at this <a href="https://difftf.readthedocs.io/en/latest/chapter2.html#parameter-hocomoco-mapping" rel="nofollow noreferrer">page of manual</a>. If you don't need extra-flexibility in the generation of TFBS predictions, it can be the simplest way to proceed.</li>
  </ol>
  