Answers.Body: <p>I do not know <code>bedops</code>, so I assume that this two-step pipe at the end of <code>bedmap</code> produces a regular bedGraph.</p>
  <p>The problem is that both <code>bedGraphToBigWig</code> and <code>bigWigToWig</code> like any of the kentUtils tools does not read or write from/to <code>stdin</code>/<code>stdout</code>. Hence, write the bedGraph to disk, then convert to BigWig, then convert to Wig. Tedious, but that's what kentUtils support -- they do not allow piping.</p>
  
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Answers.CreationDate: 2024-06-01T13:29:40.603Z
Answers.Text: Could you add the relevant command please? As it stands, this is pointing the OP in the right direction, but it isn't actually giving the answer.
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Body: <p>I was wondering how can I convert bed file to wig file.</p>
  <p>I have several bed files which look like</p>
  <pre><code>head EE88324.shortlong.frag.bed
  chr1    10003   10117   1
  chr1    10003   10138   1
  chr1    10003   10146   1
  chr1    10008   10152   1
  chr1    10009   10129   1
  chr1    10009   10130   1
  chr1    10025   10169   1
  chr1    10026   10145   1
  chr1    10030   10172   1
  chr1    10052   10245   1
  </code></pre>
  <p>Now I want convert this bed file to wig file, which should look like this, (this toy bed and wig samples are different)</p>
  <pre><code>head -n 50 S9U_ZKDN240002406-1A_H5VMFDSXC_L1_bwaM_readCounts.w1000k.wig
  fixedStep chrom=chr1 start=1 step=1000000 span=1000000
  2682
  8134
  7087
  6923
  5585
  5579
  7056
  5953
  6174
  7058
  6606
  6682
  5630
  4705
  5432
  6755
  9442
  6563
  5891
  6427
  6033
  6871
  6360
  6574
  </code></pre>
  <p>What I tried so far,</p>
  <pre><code>#bed to wig conversion
  chromsizes=&quot;~/mapF/GRCh38_chr.txt&quot;
  bedGraphToBigWig=&quot;~/KentUtils/exe/linux.x86_64/bedGraphToBigWig&quot;
  bigWigToWig=&quot;~/KentUtils/exe/linux.x86_64/bigWigToWig&quot;
  
  
  conda activate bedops_env
      bedops --partition EE88324.shortlong.frag.bed |
      bedmap --echo --mean --delim '\t' --window 1000000 --fixed 1000000 - EE88324.shortlong.frag.bed |
      <span class="math-container">$bedGraphToBigWig - $</span>chromsizes |
      $bigWigToWig - EE88324.shortlong.diff.partition.map.1MB.wig
  </code></pre>
  
Tags: <bed><ucsc><bigwig><conversion>
Title: How to convert bed to wig file!
ThreadText: # How to convert bed to wig file!
  
  (Asked by: username_0 on 2024-05-31)
  
  I was wondering how can I convert bed file to wig file.
  
  I have several bed files which look like
  
  ```
  head EE88324.shortlong.frag.bed
  chr1    10003   10117   1
  chr1    10003   10138   1
  chr1    10003   10146   1
  chr1    10008   10152   1
  chr1    10009   10129   1
  chr1    10009   10130   1
  chr1    10025   10169   1
  chr1    10026   10145   1
  chr1    10030   10172   1
  chr1    10052   10245   1
  
  ```
  
  Now I want convert this bed file to wig file, which should look like this, (this toy bed and wig samples are different)
  
  ```
  head -n 50 S9U_ZKDN240002406-1A_H5VMFDSXC_L1_bwaM_readCounts.w1000k.wig
  fixedStep chrom=chr1 start=1 step=1000000 span=1000000
  2682
  8134
  7087
  6923
  5585
  5579
  7056
  5953
  6174
  7058
  6606
  6682
  5630
  4705
  5432
  6755
  9442
  6563
  5891
  6427
  6033
  6871
  6360
  6574
  
  ```
  
  What I tried so far,
  
  ```
  #bed to wig conversion
  chromsizes="~/mapF/GRCh38_chr.txt"
  bedGraphToBigWig="~/KentUtils/exe/linux.x86_64/bedGraphToBigWig"
  bigWigToWig="~/KentUtils/exe/linux.x86_64/bigWigToWig"
  
  conda activate bedops_env
      bedops --partition EE88324.shortlong.frag.bed |
      bedmap --echo --mean --delim '\t' --window 1000000 --fixed 1000000 - EE88324.shortlong.frag.bed |
      $bedGraphToBigWig - $chromsizes |
      $bigWigToWig - EE88324.shortlong.diff.partition.map.1MB.wig
  
  ```
  
  **Tags:** bed, ucsc, bigwig, conversion
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-05-31. Score: 0
  
  I do not know `bedops`, so I assume that this two-step pipe at the end of `bedmap` produces a regular bedGraph.
  
  The problem is that both `bedGraphToBigWig` and `bigWigToWig` like any of the kentUtils tools does not read or write from/to `stdin`/`stdout`. Hence, write the bedGraph to disk, then convert to BigWig, then convert to Wig. Tedious, but that's what kentUtils support -- they do not allow piping.
  
  > **Comments:**
  > **username_2**: Could you add the relevant command please? As it stands, this is pointing the OP in the right direction, but it isn't actually giving the answer.  
  
  ---
  
  