blastz

[王睿]

Dear UCSC Genome Browser Team,
I appreciate if you can help me with the following problems.
 
I want to use the process (http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl) from the UCSC genome browser to perform pairwise genome alignment. I made a test with the genome downloaded from NCBI and perform the same pipeline. But I found the result of our alignment is about 10% different from the result of the UCSC genome browser (using same genome version). Whether there are other steps I didn't notice? Before you proceed with this process, have you processed the genome, such as soft mask, or other processing step. 
Looking forward to your reply, thank you!
Best regards,
Jinxin

[Brian Lee]

Dear Jinxin,

Similar discussions have come up in the past in our mailing list about comparing alignment results. It may be of benefit to look into the archives and search for similar discussions. Here is one such exchange: https://groups.google.com/a/soe.ucsc.edu/g/genome/c/Bc4z_IwR13g/m/Y_POER8DBwAJ

In that discussion a first question was regarding the source of the genome files, are both of the .2bit files you are using from our download server? For instance, in that archived mailing list question with a dm6 to droSim1 situation, we asked if they obtained the files from http://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/ and http://hgdownload.soe.ucsc.edu/goldenPath/droSim1/bigZips/.

Another item is to look for when running scripts is any error messages. Be sure to look for error reports that might be attempting to alert you to issues.

Here is another search of our archives for any mention of doBlastzChainNet.pl that would be useful to review: https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=doBlastzChainNet.pl

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

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