Answers.Body: <p>If the sequences you are scanning with FIMO are supported by the <a href="https://genome.ucsc.edu/cgi-bin/hgGateway" rel="nofollow noreferrer">UCSC </a> or Ensembl genome browsers you can upload the GFF file generated by FIMO as a custom track: <a href="https://genome.ucsc.edu/cgi-bin/hgCustom" rel="nofollow noreferrer">UCSC Custom Track</a>, <a href="https://useast.ensembl.org/Homo_sapiens/Info/Index" rel="nofollow noreferrer">ENSEMBL Custom Track</a>. Note that for the Ensembl website the FIMO GFF file is in GFF3 format.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-23T21:13:23.240Z
Answers.LastActivityDate: 2023-12-23T21:13:23.240Z
Answers.UserDisplayName: Charles E. Grant
Answers.Body: <p>Potential workaround: use MAST.</p>
  <p>As far as I understand, 'under the hood', so to speak, FIMO and MAST work pretty much the same. The difference might be just that FIMO focuses on scoring motifs, while MAST is scoring sequences (<a href="https://groups.google.com/g/meme-suite/c/qMSj6AdFxoM" rel="nofollow noreferrer">https://groups.google.com/g/meme-suite/c/qMSj6AdFxoM</a>)</p>
  <p>Example of FIMO output: <a href="https://web.mit.edu/meme_v4.11.4/share/doc/examples/fimo_example_output_files/fimo.html" rel="nofollow noreferrer">https://web.mit.edu/meme_v4.11.4/share/doc/examples/fimo_example_output_files/fimo.html</a></p>
  <p>Example of MAST output: <a href="https://web.mit.edu/meme_v4.11.4/share/doc/examples/mast_example_output_files/mast.html" rel="nofollow noreferrer">https://web.mit.edu/meme_v4.11.4/share/doc/examples/mast_example_output_files/mast.html</a></p>
  <p>There might be small differences in the output of the tools, but then it's up to you to see whether this is relevant for your data.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-23T20:56:14.187Z
Answers.Text: FIMO and MAST have entirely different purposes. FIMO identifies statistically significant matches to motifs in a collection of sequences. MAST identifies the sequences that have the best overall match to a collection of motifs. The output of MAST does include a cartoon showing the motif matches for a particular sequence, it only does this for the sequences that have the best overall match to ALL the motifs in the input. It won't necessarily show the  best matches to individual motifs. The typical use case for MAST is identifying promoter sequences regulated by multiple transcription factors.
Answers.UserDisplayName: Charles E. Grant
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-23T21:16:09.727Z
Answers.Text: (cont) While internally MAST does perform a step equivalent to FIMO the final MAST output is not equivalent to the FIMO output.
Answers.UserDisplayName: Charles E. Grant
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-20T15:43:47.147Z
Answers.LastActivityDate: 2023-12-20T15:43:47.147Z
Answers.UserDisplayName: Laura
Body: <p>I used FIMO to scan several of my promoter sequences for TF binding motifs. The output .tsv file gives me the motif name/sequence plus the start and stop location, how can I visualize these outputs to get a graph that shows each motif as differing length rectangles along each promoter sequence, along with a gradient that shows the p-value?</p>
  
Tags: <bed><motifs><tsv>
Title: How to visualize FIMO outputs?
ThreadText: # How to visualize FIMO outputs?
  
  (Asked by: username_0 on 2023-12-20)
  
  I used FIMO to scan several of my promoter sequences for TF binding motifs. The output .tsv file gives me the motif name/sequence plus the start and stop location, how can I visualize these outputs to get a graph that shows each motif as differing length rectangles along each promoter sequence, along with a gradient that shows the p-value?
  
  **Tags:** bed, motifs, tsv
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2023-12-23. Score: 1
  
  If the sequences you are scanning with FIMO are supported by the [UCSC](https://genome.ucsc.edu/cgi-bin/hgGateway)  or Ensembl genome browsers you can upload the GFF file generated by FIMO as a custom track: [UCSC Custom Track](https://genome.ucsc.edu/cgi-bin/hgCustom), [ENSEMBL Custom Track](https://useast.ensembl.org/Homo_sapiens/Info/Index). Note that for the Ensembl website the FIMO GFF file is in GFF3 format.
  
  
  ---
  
  ### Answer by username_2 on 2023-12-20. Score: -1
  
  Potential workaround: use MAST.
  
  As far as I understand, 'under the hood', so to speak, FIMO and MAST work pretty much the same. The difference might be just that FIMO focuses on scoring motifs, while MAST is scoring sequences (<https://groups.google.com/g/meme-suite/c/qMSj6AdFxoM>)
  
  Example of FIMO output: <https://web.mit.edu/meme_v4.11.4/share/doc/examples/fimo_example_output_files/fimo.html>
  
  Example of MAST output: <https://web.mit.edu/meme_v4.11.4/share/doc/examples/mast_example_output_files/mast.html>
  
  There might be small differences in the output of the tools, but then it's up to you to see whether this is relevant for your data.
  
  > **Comments:**
  > **username_1**: FIMO and MAST have entirely different purposes. FIMO identifies statistically significant matches to motifs in a collection of sequences. MAST identifies the sequences that have the best overall match to a collection of motifs. The output of MAST does include a cartoon showing the motif matches for a particular sequence, it only does this for the sequences that have the best overall match to ALL the motifs in the input. It won't necessarily show the  best matches to individual motifs. The typical use case for MAST is identifying promoter sequences regulated by multiple transcription factors.  
  > **username_1**: (cont) While internally MAST does perform a step equivalent to FIMO the final MAST output is not equivalent to the FIMO output.  
  
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