Liftover tool not working at UCSC

Question: Liftover tool not working at UCSC

2.2 years ago by

Hello,

I tried to convert hg18 coordinates in a BED format data with UCSC liftover and it is not working. Looks like it only works with chrN:start-end format. But I need to retain additional information in my BED file that's why I wanted to use BED format for this conversion.

Next, I also tried Galaxy liftover after uploading BED format file, but liftover tool is not recognizing database/genome build as option to select genome build is not coming up as well "from & To" options are also not showing up at liftover tool itself. Are this tool liftover working at Galaxy.

Please suggest.

Thanks.

bed ucsc liftover galaxy • 999 views

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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by indranipoddar • 0

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To have the Liftover tool in Galaxy recognize a BED input, assign the database "hg18". I just ran a test and many genomes are available to convert to from hg18. How to: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

The tool at UCSC accepts either BED or "chrN:start-end" format. The tool in Galaxy only accepts BED format. When using Galaxy, be sure to not include any content that is not in BED format or unexpected or empty results may be returned. https://wiki.galaxyproject.org/Learn/Datatypes#Bed

Both versions of the tool return just the transformed coordinates in the primary output dataset. These original BED coordinates and other fields (name, score, etc) are not retained. The other output dataset contains the original coordinates that were not mapped. This is how the tool was designed by UCSC. It is wrapped without changes to the underlying binary in Galaxy.

Best, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you for your reply.

ADD REPLY • link written 2.2 years ago by indranipoddar • 0

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