Answers.Body: <p>I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":"</p>
  
  <p>I removed ":" and it worked</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-31T10:10:17.087Z
Answers.LastActivityDate: 2019-07-31T10:10:17.087Z
Answers.UserDisplayName: Code42
Body: <p>I was trying to use <a href="https://genome.ucsc.edu/cgi-bin/hgLiftOver" rel="nofollow noreferrer">UCSC liftover tool</a> to convert human coordinates to mouse. While most of the files worked, one file didn't:</p>
  
  <pre><code>chr16   86430087    86430726    Human_chr16:86430087-86430726___element_1___positive____neural_tube[12/12]___hindbrain_(rhombencephalon)[12/12]___limb[3/12]___cranial_nerve[8/12]
  chr16   85620095    85621736    Human_chr16:85620095-85621736___element_2___negative_
  chr16   80423343    80424652    Human_chr16:80423343-80424652___element_3___negative_
  chr16   80372593    80373755    Human_chr16:80372593-80373755___element_4___positive____neural_tube[6/10]___hindbrain_(rhombencephalon)[10/10]___midbrain_(mesencephalon)[10/10]
  </code></pre>
  
  <p>Does anyone know why this bed file can only be converted to chr:start-end format but not bed4 format?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-18T15:50:03.787Z
Comments.Text: Were there any logged messages during the process?  Can you include an example that did complete the liftover?
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-31T09:49:52.083Z
Comments.Text: If you remove everything after the "Human" in each line then it works
Comments.UserDisplayName: Code42
Tags: <bed><ucsc><liftover>
Title: UCSC liftover cannot produce bed format output
ThreadText: # UCSC liftover cannot produce bed format output
  
  (Asked by: username_0 on 2019-07-18)
  
  I was trying to use [UCSC liftover tool](https://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert human coordinates to mouse. While most of the files worked, one file didn't:
  
  ```
  chr16   86430087    86430726    Human_chr16:86430087-86430726___element_1___positive____neural_tube[12/12]___hindbrain_(rhombencephalon)[12/12]___limb[3/12]___cranial_nerve[8/12]
  chr16   85620095    85621736    Human_chr16:85620095-85621736___element_2___negative_
  chr16   80423343    80424652    Human_chr16:80423343-80424652___element_3___negative_
  chr16   80372593    80373755    Human_chr16:80372593-80373755___element_4___positive____neural_tube[6/10]___hindbrain_(rhombencephalon)[10/10]___midbrain_(mesencephalon)[10/10]
  
  ```
  
  Does anyone know why this bed file can only be converted to chr:start-end format but not bed4 format?
  
  **Tags:** bed, ucsc, liftover
  
  > **Comments:**
  > **username_1**: Were there any logged messages during the process?  Can you include an example that did complete the liftover?  
  > **username_0**: If you remove everything after the "Human" in each line then it works  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2019-07-31. Score: 1 | Accepted answer
  
  I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":"
  
  I removed ":" and it worked
  
  
  ---
  
  