1. alignments between the two genomes are constructed with lastz,
formally known at blastz:
http://genome.cshlp.org/content/13/1/103.abstract
2. the alignments are chained together using the Jim Kent program: axtChain
http://www.pnas.org/content/100/20/11484.short
The resulting chain is use by liftOver to map between the genomes.
Note the usage message from liftOver included below to clarify
the meaning of ratio of bases and alignment blocks parameters.
--Hiram
Dhiral Phadke wrote:
> Hi,
>
> I want to learn the details about how the liftOver utility works. Please can
> you point me to a document describing the underlying details?
>
> What do the following input parameters for liftOver mean?
>
> Minimum ratio of bases that must remap:
> Min ratio of alignment blocks or exons that must map:
>
> What are the recommended values for these parameters when converting from
> hg18
> to mm8.
>
> Thanks a lot for your help!
>
> -Dhiral.
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.
***********************************************************************
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
-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
-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
-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
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