Question about liftOver chain file (between species)

[Dongwu Zhan]

Dear UCSC staff,

I'm a PHD student from China Forestry University, and am very grateful for your liftOver tool which help me a lot in scientific research. I see that the chain file could be acquired from either the website or from your liftOver command tools. However, if I want to transfer coordinates between species, I could only download the chain file from your website. If I would like to make chain file myself, the only way you provide is like "DoSameSpeciesLiftOver.pl" showed, transfer coordinates between same species (like mm10 to mm9). So I wonder how could I make the chain file between two very different species genome, like human to mouse (hg19 to mm9), to get a same chain file as you put in the liftOver website? Do you use blat alignment and then make the results into chain? Could you give me your variables setting in blat alignment (or if possible, some codes or pipelines would be much helpful!) Thank you very much!

Regards,

Dongwu

[Gerardo Perez]

Hello, Dongwu.

Thank you for your interest in the Genome Browser and for your liftOver chain file question.

We do have the doBlastzChainNet.pl script/process which was used to create the hg19 to mm9 liftOver chain file: https://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl. The doBlastzChainNet.pl script is focused on creating chains between two assemblies from different organisms.

We can point you towards our makedoc for hg19 to mm9 lastz run. Keep in mind this is more made for internal replication. You can find the makedoc below on git: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg19.txt#L2239

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. 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.

Gerardo Perez
UCSC Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CA%2BMR%2ByU7YYhn4oiH_PWV8V%3DW4vDpDifOPsfSN1%3D1REK0Rpvynw%40mail.gmail.com.