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

Anne Lyle annelyle at ebi.ac.uk
Mon Apr 13 09:24:21 BST 2015

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.



> 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
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