[ensembl-dev] Dev Digest, Vol 58, Issue 13
Santosh Kumar Dodda
santoshkumar.dodda at bioseed.com
Wed Apr 15 11:31:10 BST 2015
Dear Ensemble team:
I am trying to install the refseq using the perl script for VEP. I have
tried doing it for two species viz homo_sapiens and Solanum Lycopersicum,
unfortunately both the installations got failed. For you reference I am
attaching a screen shot. Please help me in this regard.
Screen shot:
[image: Inline image 1]
Regards
Santosh Kumar Dodda
India
On Tue, Apr 14, 2015 at 4:30 PM, <dev-request at ensembl.org> wrote:
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> Today's Topics:
>
> 1. Re: chain files to build cross-species coordinates conversion
> (liftover) (Matthieu Muffato)
> 2. Question about Gene Symbol in cache refseq version (namchul ghim)
> 3. Re: Question about Gene Symbol in cache refseq version
> (Will McLaren)
> 4. Re: Diferen?as entre vers?es (mag)
> 5. Ensembl Genomes Release 27 Intentions (Dan Staines)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Apr 2015 17:53:47 +0100
> From: Matthieu Muffato <muffato at ebi.ac.uk>
> Subject: Re: [ensembl-dev] chain files to build cross-species
> coordinates conversion (liftover)
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <552BF49B.5000602 at ebi.ac.uk>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Dear Juan-Pascal
>
> Even though we do process chains as part of our pairwise-alignment
> pipelines, the files are not kept, and we rather store the alignment in
> a more condensed format in the database:
>
> http://www.ensembl.org/info/docs/api/compara/compara_schema.html#genomic_align
>
> There are two options at this stage (both using the Perl / REST API):
> either dump the alignment blocks into a chain file to run liftover, or
> only use the API. They both need to write a piece of code.
>
> If you can use the Perl API, there is an example script in the
> ensembl-compara repository that you'll find useful:
>
> https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_convertBasePositionsUsingBlastzAlignments.pl
> It takes a list of human coordinates and projects them to the chimpanzee
> genome using our alignment (just change the names of the species).
>
> If you are interested in the coordinates of each alignment block, this
> other script can help:
>
> https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_accessGenomicAlignBlocks.pl
>
> Matthieu
>
> On 13/04/15 17:18, Juan Pascual Anaya wrote:
> > 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
> > <mailto:dev-request at ensembl.org>> wrote:
> >
> >
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 13 Apr 2015 09:24:21 +0100
> > From: Anne Lyle <annelyle at ebi.ac.uk <mailto: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 <mailto:dev at ensembl.org>>
> > Message-ID: <326CB180-BB1F-4218-90E6-722656215245 at ebi.ac.uk
> > <mailto: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 <mailto: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 listDev at ensembl.org <mailto:Dev at ensembl.org>
> > > Posting guidelines and subscribe/unsubscribe info:
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> >
> > ------------------------------
> >
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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> >
> > --
> >
> > Juan Pascual-Anaya, PhD
> > Research Scientist
> > Evolutionary Morphology Laboratory, RIKEN
> > 2-2-3 Minatojima-minamimachi
> > Chuo-ku, Kobe, Hyogo 650-0047
> > Japan
> >
> >
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org
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> http://lists.ensembl.org/mailman/listinfo/dev
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> >
>
> --
> Matthieu Muffato, Ph.D.
> Ensembl Compara and TreeFam Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus, Hinxton
> Cambridge, CB10 1SD, United Kingdom
> Room A3-145
> Phone + 44 (0) 1223 49 4631
> Fax + 44 (0) 1223 49 4468
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 14 Apr 2015 08:30:03 +0900
> From: namchul ghim <chulghim at gmail.com>
> Subject: [ensembl-dev] Question about Gene Symbol in cache refseq
> version
> To: Ensembl developers list <Dev at ensembl.org>
> Message-ID:
> <CANi7z4f4ES1unbNnQ34ErHhVF9VDWm99MqsK2z=
> XD5UU4id4aw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> In Refseq version, SYMBOL field is blank.
>
> How can i get SYMBOL value in cache refseq version ?
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> ------------------------------
>
> Message: 3
> Date: Tue, 14 Apr 2015 08:48:04 +0100
> From: Will McLaren <wm2 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Question about Gene Symbol in cache refseq
> version
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID:
> <
> CAMVEDX1s0CzWzjLY00qY23qxAGrrh6mULhDj8gBE2685WiGLoQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Namchul,
>
> This was fixed already (in reply to your question in fact!).
>
> Please make sure your API is up to date; if you still experience an issue
> with this, can you please provide a sample of input and the command line
> that you are using that recreates the problem?
>
> Thanks
>
> Will
>
> On 14 April 2015 at 00:30, namchul ghim <chulghim at gmail.com> wrote:
>
> > In Refseq version, SYMBOL field is blank.
> >
> > How can i get SYMBOL value in cache refseq version ?
> >
> >
> > _______________________________________________
> > 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/
> >
> >
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> ------------------------------
>
> Message: 4
> Date: Tue, 14 Apr 2015 09:05:50 +0100
> From: mag <mr6 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Diferen?as entre vers?es
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <552CCA5E.6060903 at ebi.ac.uk>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Igo,
>
> The versions represent the releases.
> Each release, we update the databases and provide a new webserver,
> retiring the older version.
> Updates can include new data, updated data, updated schemas or new
> display features.
>
> You can check what has changed for a given release on the news page:
> http://www.ensembl.org/info/website/news_by_topic.html
>
>
> Hope that helps,
> Magali
>
> On 13/04/2015 15:21, Igo Medeiros wrote:
> > What are the main differences between the databases's versions in
> > ensembl? How can i find in the documentation?
> >
> > --
> > Igo Paix?o de Medeiros
> >
> >
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
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> ------------------------------
>
> Message: 5
> Date: Tue, 14 Apr 2015 09:12:08 +0100
> From: Dan Staines <dstaines at ebi.ac.uk>
> Subject: [ensembl-dev] Ensembl Genomes Release 27 Intentions
> To: dev at ensembl.org
> Message-ID: <552CCBD8.5010708 at ebi.ac.uk>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear all,
>
> Release 27 of Ensembl Genomes is scheduled for 26th May 2015 - our
> intentions for this release can be found here:
> http://ensemblgenomes.org/info/release/27
> Please note these are intentions and are therefore not guaranteed to be
> completed for May.
>
> Best regards,
>
> Dan Staines, on behalf of the Ensembl Genomes team.
>
> --
> Dan Staines, PhD Ensembl Genomes Technical Coordinator
> EMBL-EBI Tel: +44-(0)1223-492507
> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>
>
>
> ------------------------------
>
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>
> End of Dev Digest, Vol 58, Issue 13
> ***********************************
>
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