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# Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: mapping
I currently have it displaying regions in mouse with text and a UCSC genome browser link to the corresponding human region as a track for the mapping figure.
# TODO
[X] Display track showing homology across mouse/human/maybe rat (done for mouse, won't be hard to also enable for other species)
[ ] Make it display an arrow depending on the strand (whether the query strand matches the reference
[ ] Store the homology chain file data differently (keeping it as a text file might be fine, but need to find a better place for it; currently it's just directly pointing to its path)
# Description
The idea is to add a new track to mouse/rat mapping figures that provides links to the corresponding region for humans in the UCSC Genome Browser.
This can be done using these UCSC chain files. Links to the files and an explanation about their format are below:
- Help file: https://genome.ucsc.edu/goldenPath/help/chain.html
- Mouse reference: http://hgdownload.cse.ucsc.edu/goldenpath/mm10/liftOver/
- Human reference: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/liftOver/
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