Answers.Body: <p>I think you might have changed the separator (or at least have some kind of inconsistency from the <a href="https://genome.ucsc.edu/FAQ/FAQformat.html" rel="nofollow noreferrer">required format</a>) for your file. Note that peak output files from MACS2 are variants of BED files.</p>
  
  <p>It seems you <strong>need to have a <em>tab</em> separator for this type of file.</strong></p>
  
  <p>I copied your example file and then ran <code>awk -v OFS="\t" '$1=$1' your_peaks.narrowPeaks &gt; fixed_your_peaks.narrowPeaks</code> on it. This produced a result that I was able to see in both the UCSC genome browser and IGV.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
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Answers.Text: Strangely if you simply **add** ".bed" to your file it should work (i.e. testONE_peaks_NEW2.narrowPeak.bed)
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Answers.Text: Can we do this in R?
Answers.UserDisplayName: StupidWolf
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Answers.Text: Oh. Thank you very much.
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Body: <p>I have called peaks using MACS2. Then I got a narrowPeak file like this.</p>
  
  <pre><code>1   4491713 4491913 testONE_peak_1  37  .   2.86003 3.72580 1.66717 80
  1   4492782 4493153 testONE_peak_2  27  .   2.22933 2.71107 0.82442 242
  1   4571554 4572026 testONE_peak_3  72  .   4.16005 7.21000 4.85200 282
  1   4739486 4739879 testONE_peak_4  64  .   3.63128 6.42948 4.14394 275
  1   4784848 4785061 testONE_peak_5  31  .   2.24218 3.19160 1.21569 133
  </code></pre>
  
  <p>Then I tried to visualize it in UCSC Genome browser and I got following error.</p>
  
  <pre><code>Error File 'testONE_peaks.narrowPeak' - Unrecognized format line 1 of file: 1 4491713 4491913 testONE_peak_1  37  .   2.86003 3.72580 1.66717 80 (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')
  </code></pre>
  
  <p>So I added chr to the chromosome column instead of 1 (Chromosome number). </p>
  
  <pre><code>chr1    4491713 4491913 testONE_peak_1  37  .   2.86003 3.7258  1.66717 80
  chr1    4492782 4493153 testONE_peak_2  27  .   2.22933 2.71107 0.82442 242
  chr1    4571554 4572026 testONE_peak_3  72  .   4.16005 7.21    4.852   282
  chr1    4739486 4739879 testONE_peak_4  64  .   3.63128 6.42948 4.14394 275
  chr1    4784848 4785061 testONE_peak_5  31  .   2.24218 3.1916  1.21569 133
  </code></pre>
  
  <p>When I tried to load the file again I got following error.</p>
  
  <pre><code>Error File 'testONE_peaks_NEW2.narrowPeak' - Error line 1 of custom track: thickStart out of range (chromStart to chromEnd, or 0 if no CDS)
  </code></pre>
  
  <p>Then I added following line to the top and I could load the file to UCSC Genome browser.</p>
  
  <pre><code>track type=narrowPeak name="Somite narrowPeak"
  chr1    4491713 4491913 testONE_peak_1  37  .   2.86003 3.7258  1.66717 80
  chr1    4492782 4493153 testONE_peak_2  27  .   2.22933 2.71107 0.82442 242
  chr1    4571554 4572026 testONE_peak_3  72  .   4.16005 7.21    4.852   282
  chr1    4739486 4739879 testONE_peak_4  64  .   3.63128 6.42948 4.14394 275
  chr1    4784848 4785061 testONE_peak_5  31  .   2.24218 3.1916  1.21569 133
  </code></pre>
  
  <p>But the problem is I can not see anything in the Genome browser. Only the name is there. But nothing else. Do you know what I should do?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-26T07:53:27.043Z
Comments.Text: I am struggling with the same problem, where did you add this line of code?
  awk -v OFS="\t" '$1=$1' your_peaks.narrowPeaks > fixed_your_peaks.narrowPeaks
Comments.UserDisplayName: Libby Kosolapov
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-30T19:27:13.607Z
Comments.Text: You can run this command in a command line or terminal
Comments.UserDisplayName: MudithMMBc
Tags: <rna-seq><chip-seq><ucsc><igv><macs2>
Title: How to visualize called narrowPeak files in UCSC Genome browser or IGV?
ThreadText: # How to visualize called narrowPeak files in UCSC Genome browser or IGV?
  
  (Asked by: username_0 on 2020-02-12)
  
  I have called peaks using MACS2. Then I got a narrowPeak file like this.
  
  ```
  1   4491713 4491913 testONE_peak_1  37  .   2.86003 3.72580 1.66717 80
  1   4492782 4493153 testONE_peak_2  27  .   2.22933 2.71107 0.82442 242
  1   4571554 4572026 testONE_peak_3  72  .   4.16005 7.21000 4.85200 282
  1   4739486 4739879 testONE_peak_4  64  .   3.63128 6.42948 4.14394 275
  1   4784848 4785061 testONE_peak_5  31  .   2.24218 3.19160 1.21569 133
  
  ```
  
  Then I tried to visualize it in UCSC Genome browser and I got following error.
  
  ```
  Error File 'testONE_peaks.narrowPeak' - Unrecognized format line 1 of file: 1 4491713 4491913 testONE_peak_1  37  .   2.86003 3.72580 1.66717 80 (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')
  
  ```
  
  So I added chr to the chromosome column instead of 1 (Chromosome number).
  
  ```
  chr1    4491713 4491913 testONE_peak_1  37  .   2.86003 3.7258  1.66717 80
  chr1    4492782 4493153 testONE_peak_2  27  .   2.22933 2.71107 0.82442 242
  chr1    4571554 4572026 testONE_peak_3  72  .   4.16005 7.21    4.852   282
  chr1    4739486 4739879 testONE_peak_4  64  .   3.63128 6.42948 4.14394 275
  chr1    4784848 4785061 testONE_peak_5  31  .   2.24218 3.1916  1.21569 133
  
  ```
  
  When I tried to load the file again I got following error.
  
  ```
  Error File 'testONE_peaks_NEW2.narrowPeak' - Error line 1 of custom track: thickStart out of range (chromStart to chromEnd, or 0 if no CDS)
  
  ```
  
  Then I added following line to the top and I could load the file to UCSC Genome browser.
  
  ```
  track type=narrowPeak name="Somite narrowPeak"
  chr1    4491713 4491913 testONE_peak_1  37  .   2.86003 3.7258  1.66717 80
  chr1    4492782 4493153 testONE_peak_2  27  .   2.22933 2.71107 0.82442 242
  chr1    4571554 4572026 testONE_peak_3  72  .   4.16005 7.21    4.852   282
  chr1    4739486 4739879 testONE_peak_4  64  .   3.63128 6.42948 4.14394 275
  chr1    4784848 4785061 testONE_peak_5  31  .   2.24218 3.1916  1.21569 133
  
  ```
  
  But the problem is I can not see anything in the Genome browser. Only the name is there. But nothing else. Do you know what I should do?
  
  **Tags:** rna-seq, chip-seq, ucsc, igv, macs2
  
  > **Comments:**
  > **username_1**: I am struggling with the same problem, where did you add this line of code? awk -v OFS="\t" '$1=$1' your_peaks.narrowPeaks > fixed_your_peaks.narrowPeaks  
  > **username_0**: You can run this command in a command line or terminal  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-02-12. Score: 2 | Accepted answer
  
  I think you might have changed the separator (or at least have some kind of inconsistency from the [required format](https://genome.ucsc.edu/FAQ/FAQformat.html)) for your file. Note that peak output files from MACS2 are variants of BED files.
  
  It seems you **need to have a *tab* separator for this type of file.**
  
  I copied your example file and then ran `awk -v OFS="\t" '$1=$1' your_peaks.narrowPeaks > fixed_your_peaks.narrowPeaks` on it. This produced a result that I was able to see in both the UCSC genome browser and IGV.
  
  > **Comments:**
  > **username_2**: Strangely if you simply **add** ".bed" to your file it should work (i.e. testONE_peaks_NEW2.narrowPeak.bed)  
  > **username_3**: Can we do this in R?  
  > **username_0**: Oh. Thank you very much.  
  
  ---
  
  