[Genome] how can I change the chain format to psl and then to axt ?

[Ann Zweig]

Hello Xiaolu,

	We do have a program that you can use that will convert chain files to axt 
files.  You will want to start with the flat chain files located on our download 
server here:

http://hgdownload.cse.ucsc.edu/downloads.html

	For example, if you are looking for the chain file from the latest human 
assembly to many other assemblies you will find them here:

http://hgdownload.cse.ucsc.edu/downloads.html#human

Then choose your pairwise species from the list in "Pairwise Alignments:"

	So, the chain file for human (hg18) to mouse (mm9) you would follow this link: 
"Human/Mouse (mm9) pairwise alignments", and choose this file: 
hg18.mm9.all.chain.gz

	Read about the format of the chain files in this FAQ:
http://genome.ucsc.edu/goldenPath/help/chain.html

	Once you have the chain file you need, you can use the chainToAxt program to 
convert it to axt format.

chainToAxt - Convert from chain to axt file
usage:
    chainToAxt in.chain tNibDir qNibDir out.axt
options:
    -maxGap=maximum gap sized allowed without breaking, default 100
    -maxChain=maximum chain size allowed without breaking, default 1073741823
    -minScore=minimum score of chain
    -minId=minimum percentage ID within blocks
    -bed  Output bed instead of axt


	The Genome Browser and associated programs are free for academic, nonprofit, 
and personal use. A license is required for commercial use.

How to download the software: http://genome.cse.ucsc.edu/FAQ/FAQlicense#license3

You can obtain the source tree either via CVS:
	http://genome.ucsc.edu/admin/cvs.html
or a zip file:
	http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

Please note the build instructions:
	http://genome.ucsc.edu/admin/jk-install.html

	All of the kent utilities output their usage message and command line options 
by running them with no arguments.



Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Xiaolu.Huang at UCHSC.edu wrote:
> Dear bioinformaticians at ucsc genome,
>  
> Thanks for your previous prompt reply! I need to change the chain files to axt files. The only way I can find is the chaintopsl, but I do not know how to download it. also in the 
> "usage: 
>    chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl 
>   Where tSizes and qSizes are tab-delimited files with 
>        <seqName><size> columns. "
> 
> I am afraid that I do not quite know what the tSizes and qSizes files should be.
> 
> Could you show me a way to convert a chain table file to axt files?
> 
> Thanks!
> 
> Xiaolu 
> 
>  
> 
>  
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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