<div dir="ltr">Dear Matthieu,<div><br></div><div>I have some experience using the core API, but didn't know about the compara schema for this. Both scripts are quite useful for what I need. Thank you very much!</div><div><br></div><div>Best,</div><div>Juan<br><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 14, 2015 at 8:00 PM, <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span> wrote:</div><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Date: Mon, 13 Apr 2015 17:53:47 +0100<br>
From: Matthieu Muffato <<a href="mailto:muffato@ebi.ac.uk">muffato@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] chain files to build cross-species<br>
coordinates conversion (liftover)<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:552BF49B.5000602@ebi.ac.uk">552BF49B.5000602@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset=windows-1252; format=flowed<br>
<br>
Dear Juan-Pascal<br>
<br>
Even though we do process chains as part of our pairwise-alignment<br>
pipelines, the files are not kept, and we rather store the alignment in<br>
a more condensed format in the database:<br>
<a href="http://www.ensembl.org/info/docs/api/compara/compara_schema.html#genomic_align" target="_blank">http://www.ensembl.org/info/docs/api/compara/compara_schema.html#genomic_align</a><br>
<br>
There are two options at this stage (both using the Perl / REST API):<br>
either dump the alignment blocks into a chain file to run liftover, or<br>
only use the API. They both need to write a piece of code.<br>
<br>
If you can use the Perl API, there is an example script in the<br>
ensembl-compara repository that you'll find useful:<br>
<a href="https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_convertBasePositionsUsingBlastzAlignments.pl" target="_blank">https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_convertBasePositionsUsingBlastzAlignments.pl</a><br>
It takes a list of human coordinates and projects them to the chimpanzee<br>
genome using our alignment (just change the names of the species).<br>
<br>
If you are interested in the coordinates of each alignment block, this<br>
other script can help:<br>
<a href="https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_accessGenomicAlignBlocks.pl" target="_blank">https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_accessGenomicAlignBlocks.pl</a><br>
<br>
Matthieu<br>
<br>
On 13/04/15 17:18, Juan Pascual Anaya wrote:<br>
> Hi Anne,<br>
><br>
> Thank you very much for your reply!<br>
><br>
> According to those links that I sent about the pairwise alignments I'm<br>
> interested in, you can read the following:<br>
><br>
> "After running LastZ, the raw LastZ alignment blocks are chained<br>
> according to their location in both genomes. During the final netting<br>
> process, the best sub-chain is chosen in each region on the reference<br>
> species."<br>
><br>
> So, I thought that those chain files were already done and available<br>
> somewhere.<br>
><br>
> I'm using all my genome coordinates from Ensembl (e74), so I guess I<br>
> could also use your Assembly Converter tool, but I would still need the<br>
> chain files, right? Here:<br>
><br>
> <a href="http://www.ensembl.org/info/docs/webcode/mirror/tools/assembly_converter.html" target="_blank">http://www.ensembl.org/info/docs/webcode/mirror/tools/assembly_converter.html</a><br>
><br>
> when I try to go to the FTP site where the "current chain files" are,<br>
> the site doesn's exist, so I thought that this method is out of date.<br>
><br>
> If the Compara team has more info about this, that would be great!<br>
><br>
> Thanks!<br>
> Juan<br>
><br>
><br>
><br>
> On Mon, Apr 13, 2015 at 8:00 PM, <<a href="mailto:dev-request@ensembl.org">dev-request@ensembl.org</a><br>
> <mailto:<a href="mailto:dev-request@ensembl.org">dev-request@ensembl.org</a>>> wrote:<br>
><br>
><br>
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> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Mon, 13 Apr 2015 09:24:21 +0100<br>
> From: Anne Lyle <<a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a> <mailto:<a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a>>><br>
> Subject: Re: [ensembl-dev] chain files to build cross-species<br>
> coordinates conversion (liftover)<br>
> To: Ensembl dev list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>>><br>
> Message-ID: <<a href="mailto:326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk">326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk</a><br>
> <mailto:<a href="mailto:326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk">326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk</a>>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi Juan<br>
><br>
> We currently only produce chain files (for our own Assembly<br>
> Converter) for those species where we?ve done an assembly mapping<br>
> through our core pipeline. Perhaps our compara team can chime in<br>
> with whether it?s feasible to create them based on pairwise alignments.<br>
><br>
> Cheers<br>
><br>
> Anne<br>
><br>
><br>
> > On 12 Apr 2015, at 09:42, Juan Pascual Anaya <<a href="mailto:jpascualanaya@gmail.com">jpascualanaya@gmail.com</a> <mailto:<a href="mailto:jpascualanaya@gmail.com">jpascualanaya@gmail.com</a>>> wrote:<br>
> ><br>
> > Hi Ensembl team,<br>
> ><br>
> > 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:<br>
> ><br>
> > Mouse-Chicken pairwise alignment<br>
> ><a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633</a><br>
> <<a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633</a>><br>
> ><br>
> > Chicken-Turtle pairwise alignment<br>
> ><a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657</a><br>
> <<a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657</a>><br>
> ><br>
> > 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?<br>
> ><br>
> > Thank you very much,<br>
> > Juan<br>
> ><br>
> > _______________________________________________<br>
> > Dev mailing <a href="mailto:listDev@ensembl.org">listDev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>><br>
> > Posting guidelines and subscribe/unsubscribe info:<a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> > Ensembl Blog:<a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
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> ------------------------------<br>
><br>
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><br>
> --<br>
><br>
> Juan Pascual-Anaya, PhD<br>
> Research Scientist<br>
> Evolutionary Morphology Laboratory, RIKEN<br>
> 2-2-3 Minatojima-minamimachi<br>
> Chuo-ku, Kobe, Hyogo 650-0047<br>
> Japan<br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
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><br>
<br>
--<br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara and TreeFam Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus, Hinxton<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room A3-145<br>
Phone <a href="tel:%2B%2044%20%280%29%201223%2049%204631" value="+441223494631">+ 44 (0) 1223 49 4631</a><br>
Fax <a href="tel:%2B%2044%20%280%29%201223%2049%204468" value="+441223494468">+ 44 (0) 1223 49 4468</a></blockquote></div>
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