Question: How To Generate Axtnet File?
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gravatar for Ge
7.7 years ago by
Ge80
Switzerland
Ge80 wrote:

How to generate the axtNet file? Such as on UCSC http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsDanRer7/. According to UCSC's help page, "axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC. " Is there any detailed instruction I can follow? Because I want this file for two assemblies, and UCSC does not provide it. Thanks.

ucsc • 2.4k views
ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Ge80
0
gravatar for Ge
7.7 years ago by
Ge80
Switzerland
Ge80 wrote:

I found it. https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008710.html http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto#doBlastzChainNet.pl

ADD COMMENTlink written 7.7 years ago by Ge80
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