[Genome] correction of chunk coordinates in blastz alignments

[Ann Zweig]

Hello J.L.,

	The automation scripts that Hiram pointed you to contain all of the 
detailed information you are asking about.  All of the kent utilities 
output their usage message and command line options by running them with 
no arguments.

	Run blastz-normalizeLav on each individual lav file output from blastz. 
  'cat' together these individual results to produce the final answer.

Regards,

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




Wang JianLi wrote:
> 
> Thank you. I have found the blastz-normalizeLav. But I didn't figure out what parameters I need to specify. 
>  
> Does the blastz-normalizeLav read all the .lav files at one run?
>  
> Thanks.
>  
>  
> 
> ________________________________
> 
> From: Hiram Clawson [mailto:hiram at soe.ucsc.edu]
> Sent: Thu 3/6/2008 10:12 PM
> To: Wang JianLi
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] correction of chunk coordinates in blastz alignments
> 
> 
> 
> Good Morning J.L.:
> 
> All of the tools required to run the blastz sequence are in the
> kent source tree.  Fetch the source tree:
> http://genome.ucsc.edu/admin/cvs.html
> and then look at the file:
>         src/hg/utils/automation/doBlastzChainNet.pl
> and library there: HgAutomate.pm
> 
> See also articles about this subject in the genomewiki.ucsc.edu
> 
> --Hiram
> 
> Wang JianLi wrote:
>> Hi All,
>>
>> I split human genomic sequences into chunks with size 10M, and overlap size 10K, and run blastz to align each chunk with another genome. Then I have a number of .lav files after the blastz. I am not sure how I can piece them together, to correct the coordicates of the sequence chunks. As in each chunk, the sequence coordinate will start from 1, but in the original chromosome sequence, this coordinate should be adjusted by the size of chunks and overlap region.
>>
>> I read that blastz-normalizeLav written by Scott Schwartz can do that. Does anybody know where to get that script?
>>
>> Thank you.
>>
>> Regards,
>> J.L
> 
> 
> 
> Note: This message may contain confidential information. If this email has been sent to you by mistakes, please notify the sender and delete it immediately. Thank you.
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome