Hi, Jennifer
Thank you very much for the detailed description, I am now clear about this.
Regards,
Zhi-Qiang
2009/11/10 Jennifer Jackson <[email protected]>:
> Hello,
>
> The wording is confusing, but it has to do with the way that the data is
> processed. For practical purposes, use the command line like this:
>
> liftOver hg18_oldFile hg18ToRn4.over.chain rn4_newFile unMapped
>
> where the over.chain file is the liftOver file from Downloads
>
> hg18_oldFile are the coordinates from hg18 that are known and that you want
> to map
>
> rn4_newFile are the coordinates from rn4 that are unknown and that you want
> to find out, based on the files above. Note that you are supplying a file
> name here - no data or actual file should exist at the time the command is
> first run.
>
> unMapped are the coordinates from hg18_oldFile that were unable to be mapped
> using the over.chain file and the parameters supplied to the program. For
> cross-species liftOver, we general lower -minmatch=0.1 and add in -multiple,
> to maximise the number of locations mapped, however this can produce a large
> number of spurious hits. Try also adding in a -minChain or -minSize length
> for either the query (hg18) or the target (rn4) - 300, 500, or 1000 - test
> and see which work best for you to reduce the unwanted noise from short or
> non-specific matches. Or, run a few cycles, starting out strict, then making
> the parameters more permissive with the unMapped set based on the failure
> reason.
>
> We hope this helps.
> Jennifer Jackson
>
>
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