Good Morning Kirill:
Please note the description of the chain file format:
http://genome.ucsc.edu/goldenPath/help/chain.html
as found from:
http://genome.ucsc.edu/FAQ/FAQformat
--Hiram
Kirill Golosov wrote:
> Hello
>
> Could somebody describe the internal format of *.over.chain files used by
> liftOver?
>
> For example such file can contain following lines:
>
> ##matrix=axtChain 16
> 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
> chain 17776980940 chr1 195109612 + 3000000 195109612 chr1 194923535 + 3036540
> 194923535 1
> 4858 6 0
> 215772 0 1
> 141108 2 0
> 504 1 0
> 197 1 0
> 1993 1 0
> 36 100 7
> 10455 0 1
> 1310 107 59
> ...
>
> Thank you very much
>
> Kirill
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