Liftover from goat to human

[Gregory Costain]

Dear colleagues, 

We're interested in lifting over a set of coordinates from goat (GCF_001704415.1; Capra hircus) to human. Is there a way to do this through UCSC Browser that we're missing?

Thanks! Greg Costain

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[Gerardo Perez]

Hello, Greg.

Thank you for your interest in the Genome Browser and for sending your inquiry.

We do offer the UCSC LiftOver tool to move annotations from one assembly to another. We have made the following chain files available on our download server:

GCF_001704415.1 → hg38: https://hgdownload.soe.ucsc.edu/goldenPath/GCF/001/704/415/GCF_001704415.1/liftOver/GCF_001704415.1ToHg38.over.chain.gz

hg38 → GCF_001704415.1: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToGCF_001704415.1.over.chain.gz

You can download the ‘liftOver’ utility from the downloads page, https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. You can then find ‘liftOver’ under the directory that matches your operating system. For example, here is the direct link for linux:
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver

You can run a utility on its own to see a help message, e.x.

$ ./liftOver
liftOver - Move annotations from one assembly to another
usage:
   liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

***********************************************************************
WARNING: liftOver was only designed to work between different
         assemblies of the same organism. It may not do what you want
         if you are lifting between different organisms. If there has
         been a rearrangement in one of the species, the size of the
         region being mapped may change dramatically after mapping.
***********************************************************************

options:
   -minMatch=0.N Minimum ratio of bases that must remap. Default 0.95
   -gff  File is in gff/gtf format.  Note that the gff lines are converted
         separately.  It would be good to have a separate check after this
         that the lines that make up a gene model still make a plausible gene
         after liftOver
   -genePred - File is in genePred format
   -sample - File is in sample format
   -bedPlus=N - File is bed N+ format (i.e. first N fields conform to bed format)
   -positions - File is in browser "position" format
   -hasBin - File has bin value (used only with -bedPlus)
   -tab - Separate by tabs rather than space (used only with -bedPlus)
   -pslT - File is in psl format, map target side only
   -ends=N - Lift the first and last N bases of each record and combine the
             result. This is useful for lifting large regions like BAC end pairs.
   -minBlocks=0.N Minimum ratio of alignment blocks or exons that must map
                  (default 1.00)
   -fudgeThick    (bed 12 or 12+ only) If thickStart/thickEnd is not mapped,
                  use the closest mapped base.  Recommended if using 
                  -minBlocks.
   -multiple               Allow multiple output regions
   -noSerial               In -multiple mode, do not put a serial number in the 5th BED column
   -minChainT, -minChainQ  Minimum chain size in target/query, when mapping
                           to multiple output regions (default 0, 0)
   -minSizeT               deprecated synonym for -minChainT (ENCODE compat.)
   -minSizeQ               Min matching region size in query with -multiple.
   -chainTable             Used with -multiple, format is db.tablename,
                               to extend chains from net (preserves dups)
   -errorHelp              Explain error messages

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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