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Question: Using Lift-Over to convert GRCh37 to GRCh38. "no option available" for converting "To" field
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gravatar for sbpateldoc
18 months ago by
sbpateldoc • 0
sbpateldoc • 0 wrote:

I have a bed file in GRCh37 coordinates that I want to convert to GRCh38. I am trying to use lift-Over, so I first converted to a GFF. However, the converting "To" field states "no options available" (i.e. no drop down appears when I click it). Why is this? I hope this does not mean that I have to download a genome build, does it?

BTW: I didn't see this same/similar question posted on BioStars, but if it has, my apologies and please point me in the right direction.

Thanks, Snehal
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by sbpateldoc • 0
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gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Data from this tool is only available from UCSC and is based on the UCSC-sourced genome builds. The tool interprets the dataset assigned "database" metadata for the input BED/GTF and presents mapping options when available.

If the data are not assigned to the UCSC version of the build, then no liftOver data will be available in the tool. The underlying mapping data is generated by UCSC as part of their "Conservation" track. It is the only stable source of the data publicly available that I know of.

In addition, not all UCSC genome builds have this information available and/or there is available data but it has not been added to Galaxy at http://usegalaxy.org (yet). I am not sure what genome you are using, but hg19 to hg38 and mm9 to mm10 are both available (and the reverse).

Data that is not based on the UCSC-version of the genome build cannot just be assigned to a UCSC database. The identifiers need to be modified first (when that is even possible), otherwise, the liftOver tool will error. More about genomes and chromosome identifiers. https://galaxyproject.org/support/chrom-identifiers/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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