Some Question About Lastz And Alignment

[李梓锋Lee_ZiFung]

Hi，

     If I want to make alignment file between mouse genome data and Zoker genome data,and make the file Iike “chr1.mouse.zoker.maf”.Should I use the chromosome one from the mouse align the zoker genome which  include lots of contigs?

    And the parameters of lastz what I used is  

:lastz  ./chr1.fa  zoker/fa/*.fa   - -step=20 - -seed=12 of 19 - -transition - -gap=400,30  - -hspthresh=3000 - -gappedthresh=2300 - -inner=2200  - -format=maf > ../chr1.maf 

Whether other parameters need to be added?  

Looking forward to your answer

 

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发自我的 iPad

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and for your question about creating MAF files.

Running whole-genome alignments can be a complicated process, and the following wiki page on the topic can help, http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto. The doBlastzChainNet.pl script will create a pairwise alignment and the lastz parameters are defined inside a DEF file. Some example lastz parameters used for human can be found on the following wiki pages:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#lastz_parameter_file
http://genomewiki.ucsc.edu/index.php/Lastz_DEF_file_parameters

We also recommend contacting the lastz help desk for more specific help on lastz parameters, lastz...@lists.bx.psu.edu.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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