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terdon ♦
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UCSC lifeoverliftover cannot produce bed format outputsoutput

I was trying to use UCSC liftover toolUCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didntdidn'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]

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?

UCSC lifeover cannot produce bed format outputs

I was trying to use UCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didnt:

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?

UCSC liftover cannot produce bed format output

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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UCSC lifeover cannot produce bed format outputs

I was trying to use UCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didnt:

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?