[ensembl-dev] Confused by the target/query core database in whole genome alignment based gene build

Wed Apr 18 14:32:29 BST 2012

Hi Zhang

In the PAIR_ALIGNER module, the reference_collection_name corresponds to 
the target_collection_name. In the other two modules (CHAIN_CONFIG and 
NET_CONFIG), the reference_collection_name corresponds to the 
query_collection_name. Part of the reason to change the name was to be 
able to use the same name for all 3 modules.

In short, just use the same genome as the reference_collection_name for 
all 3.

Note that we have changed the way we run this pipeline and this 
configuration file is not longer supported. The documentation for the 
new pipeline is available under ensembl-compara/docs/README-pairaliger. 
Obviously, you can still use ensembl_64 API and pipeline for as long as 
you want.

I hope this helps

Javier

On 18/04/12 13:33, Zhang Di wrote:
> Thank you, Javier
>
> You mean I should set some thing like below in the compara_2x.conf to 
> prepare the compara_db for gene projection.
>
>     {
>     TYPE => PAIR_ALIGNER,
>     reference_collection_name => 'human',
>     non_reference_collection_name => 'my_genome',
>     }
>     {
>     TYPE => CHAIN_CONFIG,
>     non_reference_collection_name => 'human',
>     reference_collection_name => 'my_genome',
>     }
>     {
>     TYPE => NET_CONFIG,
>     non_reference_collection_name => 'human',
>     reference_collection_name => 'my_genome',
>     }
>
> By the way, I'm using ensembl-compara version 64.
>
> On Wed, Apr 18, 2012 at 4:57 PM, Javier Herrero <jherrero at ebi.ac.uk 
> <mailto:jherrero at ebi.ac.uk>> wrote:
>
>     Dear Zhang
>
>     The query/target naming has always been quite confusing in the
>     pairwise alignment pipeline. When running an alignment, you use a
>     sequence (query) to look for similar regions in another sequence
>     (target genome). The pairwise alignment pipeline has three major
>     steps: (a) raw alignments; (b) chaining; and (c) netting. The
>     chaining step tries to link all the raw alignments that are in the
>     same order and orientation to create a longer structure called
>     chain. The netting step requires you to define a target genome
>     such as the so-called nets are the subset of chains that form the
>     best-in-genome alignment. In other words, the final set will
>     provide you for each bp of the target genome with the best match
>     on the other genome.
>
>     As I said earlier, query and target are often times confusing
>     terms. To make the situation worse, we use to run the pipeline
>     such as the query for the raw alignment step was the target for
>     the chaining and netting steps and vice versa. We have now changed
>     the way we refer to both sequences and call them reference and
>     non-reference genomes. We find that nomenclature less confusing.
>
>     Kind regards
>
>     Javier
>
>
>     On 18/04/12 09:43, Dan Barrell wrote:
>>     Hi,
>>
>>     The document low_coverage_gene_build.txt is quite old and
>>     possibly very out of date as we no longer build on low coverage
>>     genomes in Ensembl. As far as I know, the reason that the
>>     semantics of the reference and target terms got swapped is to do
>>     with the importance of directionality in a Net. When dealing with
>>     the low coverage genomes the idea was that they wanted the
>>     species they were projecting onto as the reference because it is
>>     important that each bp in the target species aligns to at most
>>     one location in the reference species.
>>
>>     I would suggest you also look at the Ensembl Compara
>>     documentation which is maintained here:
>>
>>     ensembl-compara/docs/README-low-coverage-genome-aligner
>>
>>     Dan
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>     On 17/04/12 12:47, Zhang Di wrote:
>>>     Hi,
>>>
>>>     I'm using ensembl pipeline for projection genebuild.
>>>
>>>     when I read the doc low_coverage_gene_build.txt, I was confused
>>>     by the target/query genome terms.
>>>
>>>     It calls our newly sequenced genome the target, calls the
>>>     reference genome the query.
>>>
>>>     It is contrary to lastz terms where target means reference and
>>>     query means our sequences.
>>>
>>>     It just OK if I stick to this convention.
>>>
>>>     However,
>>>
>>>     In the whole genome alignment section in the same doc,
>>>
>>>     It says that :
>>>
>>>         "each bp in the target genome should be represented at most
>>>     once."
>>>
>>>     What does it mean by saying "target"?
>>>
>>>     lastz-chain-net produces the lastz termed "target genome" with
>>>     this property.
>>>
>>>     Does it mean that I should set my genome as the reference
>>>     genome, while the genome from ensembl such as "human" as the
>>>     non-reference in the compara/hive pipeline?
>>>
>>>     I can project human genes to my genome with this somewhat weird
>>>     setting, in the next wga2genes step?
>>>
>>>     Some slice of human genome containing genes may exist several
>>>     times in the compara_db, how can it produce gene projection
>>>     right here?
>>>
>>>
>>>     Thanks
>>>
>>>     Best Reguards
>>>
>>>     -- 
>>>     Zhang Di
>>>
>>>
>>>     _______________________________________________
>>>     Dev mailing listDev at ensembl.org  <mailto:Dev at ensembl.org>
>>>     List admin (including subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>>>     Ensembl Blog:http://www.ensembl.info/
>>
>>
>>
>>
>>     _______________________________________________
>>     Dev mailing listDev at ensembl.org  <mailto:Dev at ensembl.org>
>>     List admin (including subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>>     Ensembl Blog:http://www.ensembl.info/
>
>     -- 
>     Javier Herrero, PhD
>     Ensembl Coordinator and Ensembl Compara Project Leader
>     European Bioinformatics Institute (EMBL-EBI)
>     Wellcome Trust Genome Campus, Hinxton
>     Cambridge - CB10 1SD - UK
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     List admin (including subscribe/unsubscribe):
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> -- 
> Zhang Di
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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