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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?

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  • $\begingroup$ Were there any logged messages during the process? Can you include an example that did complete the liftover? $\endgroup$
    – Bioathlete
    Commented Jul 18, 2019 at 15:50
  • $\begingroup$ If you remove everything after the "Human" in each line then it works $\endgroup$
    – Code42
    Commented Jul 31, 2019 at 9:49

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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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