liftover files of Bos_taurus_UMD_3.1/bosTau6

[wenjuan.zhu]

Hi,

 

Thanks for your time.

Recently, I would like to research Bos_taurus_UMD_3.1, and I find Bos_taurus_UMD_3.1/bosTau6 is very close to horse and dog.

So, I would like to know corresponding base of horse to Bos_taurus_UMD_3.1.

It will be very nice if you provide "bosTau6ToequCab2.over.chain.gz" and "bosTau6TocanFam3.over.chain.gz".

Could you help me ? It will help me a lot.

 

Thanks for your help.

Looking forward to your reply.

 

Best,

 

Wenjuan ZHU

[Jonathan Casper]

Hello Wenjuan,

Thank you for your question about liftOver files for the bosTau6 assembly. We currently have a liftOver file for bosTau6ToCanFam3.over.chain.gz on our test download server at http://hgdownload-test.soe.ucsc.edu/goldenPath/bosTau6/liftOver/, but please use discretion with this file as it has not yet been reviewed by our quality assurance staff. One of our engineers is working on a bosTau6 to equCab2 liftOver now, and we will inform you as soon as it is ready.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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[朱文娟(Wenjuan.zhu)]

Hi Jonathan ,

Thanks for your help. It helps me a lot.

But I have a question about liftover.  following sentence is liftover warning. For now, I want to lifting between different organisms and using  this information to analyisis and finally publish a paper. But based on your warning , I am a little worrid about this part. 

"liftOver was only designed to work between different assemblies of the same organism. It may not do what you want if you are lifting between different organisms. If there has been a rearrangement in one of the species, the size of the region being mapped may change dramatically after mapping."

Could you tell me whether it can be accepted by reviewer (IF>20)  or not ? It will take some time if I used lastz to compare two genome sequence, which is normal methods to get ancestral allele.

If it is convient for you, Could you add two liftover files (bosTau6 to oviAri3 and bosTau6 to susScr3) ?

Thanks.

Looking forward to your reply.

Best,

wenjuan ZHU

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发件人: Jonathan Casper [jca...@soe.ucsc.edu]
发送时间: 2014年10月29日 1:36
收件人: 朱文娟(Wenjuan.zhu)
Cc: genome
主题: Re: [genome] liftover files of Bos_taurus_UMD_3.1/bosTau6

[Jonathan Casper]

Hello Wenjuan,

The liftOver chains for bosTau6 <-> equCab2, bosTau8 <-> equCab2, and bosTau6 <-> canFam3 are now all available on our test download server at http://hgdownload-test.soe.ucsc.edu. They have passed review by our QA department, and will be available for download from our main server at http://hgdownload.soe.ucsc.edu at the beginning of next week.

I'm sorry to say that I cannot tell you whether your reviewer will like your results or not - that is entirely the decision of the reviewer. One of our engineers notes that the liftOver chains we provide are already done with
lastz and are applicable to cross species comparisons. The engineer continues, however, to say that lifting is a different job than analyzing ancestral relationships. You may need to run your own scientific calculations for that purpose.

Unfortunately, we do not have the resources to continue building liftOver chains immediately upon request. We do provide liftOver chains from the bosTau7 cow assembly to the sheep and pig genomes: bosTau7ToOviAri3.over.chain.gz is available on our test download server at http://hgdownload-test.soe.ucsc.edu (please use discretion with this file, as it has not yet been reviewed by our quality assurance team), and bosTau7ToSusScr2.over.chain.gz is available on our main download server at http://hgdownload.soe.ucsc.edu. If you are interested in creating other liftOver files yourself, we provide an overview of how to build your own liftOver chains at http://genomewiki.ucsc.edu/index.php/LiftOver_Howto.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group