[ensembl-dev] chain files to build cross-species coordinates conversion (liftover)

[Juan Pascual Anaya]

Hi Anne,

Thank you very much for your reply!

According to those links that I sent about the pairwise alignments I'm
interested in, you can read the following:

"After running LastZ, the raw LastZ alignment blocks are chained according
to their location in both genomes. During the final netting process, the
best sub-chain is chosen in each region on the reference species."

So, I thought that those chain files were already done and available
somewhere.

I'm using all my genome coordinates from Ensembl (e74), so I guess I could
also use your Assembly Converter tool, but I would still need the chain
files, right? Here:

http://www.ensembl.org/info/docs/webcode/mirror/tools/assembly_converter.html

when I try to go to the FTP site where the "current chain files" are, the
site doesn's exist, so I thought that this method is out of date.

If the Compara team has more info about this, that would be great!

Thanks!
Juan



On Mon, Apr 13, 2015 at 8:00 PM, <dev-request at ensembl.org> wrote:

>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.ensembl.org/pipermail/dev/attachments/20150413/ce034369/attachment-0001.htm
> >
>
> ------------------------------
>
> Message: 2
> Date: Mon, 13 Apr 2015 09:24:21 +0100
> From: Anne Lyle <annelyle at ebi.ac.uk>
> Subject: Re: [ensembl-dev] chain files to build cross-species
>         coordinates     conversion (liftover)
> To: Ensembl dev list <dev at ensembl.org>
> Message-ID: <326CB180-BB1F-4218-90E6-722656215245 at ebi.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Juan
>
> We currently only produce chain files (for our own Assembly Converter) for
> those species where we?ve done an assembly mapping through our core
> pipeline. Perhaps our compara team can chime in with whether it?s feasible
> to create them based on pairwise alignments.
>
> Cheers
>
> Anne
>
>
> > On 12 Apr 2015, at 09:42, Juan Pascual Anaya <jpascualanaya at gmail.com>
> wrote:
> >
> > Hi Ensembl team,
> >
> > I am currently doing a comparative analysis of some ChIP-seq datasets
> between mouse, chicken and turtle (P. sinensis). Therefore, I was
> interested in getting a cross-species coordinate conversion, like assembly
> converter or liftover. I've seen that you have these two pairwise
> alignments done:
> >
> > Mouse-Chicken pairwise alignment
> > http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633 <
> http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633>
> >
> > Chicken-Turtle pairwise alignment
> > http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657 <
> http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657>
> >
> > So, I was wondering if I could get the best subset of chains from your
> LASTZ-net results (i.e., the liftover chain files) so that I can do myself
> a liftOver. I have not seen this files for download in the Ensembl webpage,
> so could you let me know how to get them?
> >
> > Thank you very much,
> > Juan
> >
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.ensembl.org/pipermail/dev/attachments/20150413/09f0daa9/attachment-0001.htm
> >
>
> ------------------------------
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
> --

Juan Pascual-Anaya, PhD
Research Scientist
Evolutionary Morphology Laboratory, RIKEN
2-2-3 Minatojima-minamimachi
Chuo-ku, Kobe, Hyogo 650-0047
Japan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150414/7e7855d7/attachment.html>