<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>

CC BY-SA 4.0
2019-07-31T10:10:17.087Z
2019-07-31T10:10:17.087Z
Code42
<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>

CC BY-SA 4.0
2019-07-18T15:50:03.787Z
Were there any logged messages during the process?  Can you include an example that did complete the liftover?
Bioathlete
CC BY-SA 4.0
2019-07-31T09:49:52.083Z
If you remove everything after the "Human" in each line then it works
Code42
<bed><ucsc><liftover>
UCSC liftover cannot produce bed format output
# UCSC liftover cannot produce bed format output

(Asked by: username_0 on 2019-07-18)

I was trying to use UCSC liftover tool 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  

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## 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


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