Question: Liftover tool not working at UCSC
0
gravatar for indranipoddar
17 months ago by
indranipoddar0 wrote:

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 • 558 views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson24k • written 17 months ago by indranipoddar0
0
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 17 months ago by Jennifer Hillman Jackson24k

Thank you for your reply.

ADD REPLYlink written 17 months ago by indranipoddar0
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