rtracklayer::liftOver parameters (minMatch)
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Nik dAK ▴ 10
@nik-dak-15517
Last seen 5.1 years ago

I have a question regarding the parameters available at the command line version but not in R.

Is there a possibility to for example alter the minMatch value (Minimum ratio of bases that must remap)?

Apparently this value adapts automatically from 0.95 default to 0.1 when using a chain for different species (in my case hg19ToMm10.over.chain) in R like it does on the webpage.

Anyways it would be great to manually adjust this value in R.

(I am aware that pslMap is maybe a better idea)

Thanks!

Best wishes,

Nik

 

rtracklayer liftOver parameters minMatch • 1.4k views
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@michael-lawrence-3846
Last seen 2.9 years ago
United States

I could look into it, but no promises. The rtracklayer liftOver is a complete reimplementation of the UCSC liftover tool, which is only freely available for academic use. I've avoided even looking at the liftover source code.

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