[ensembl-dev] Get the gaps of a given assembly

[Sarah Djebali]

Hi Javier,

Thanks for your answer, but is there a simpler way ( I am afraid I am not
so advanced in communicating with the ensembl database)? or maybe I should
send this email to another mailing list?

thanks
sarah


On Thu, Apr 18, 2013 at 3:23 PM, Javier Herrero <jherrero at ebi.ac.uk> wrote:

>  Hi Sarah
>
> One way to get these gaps is to get a slice for a whole chromosome and
> project the slice to the "seqlevel" coordinate system. The method will
> return a list reference of Bio::EnsEMBL::ProjectionSegment objects.
> Anything not covered by these ProjectionSegments are assembly gaps.
>
> Javier
>
>
> On 18/04/13 14:17, Sarah Djebali wrote:
>
>   Dear developpers,
>
>  I am doing a transcriptome analysis of different species over the time
> (ie for different ensembl versions), and I need to know where the gaps are
> located for different assemblies of different species, is there an easy way
> to do this automatically?
>
>  I would need in particular the gaps for:
> - Caenorhabditis_elegans WBcel215
> - Caenorhabditis_elegans WS220
> - Saccharomyces_cerevisiae EF2
> - Saccharomyces_cerevisiae EF3
> - Saccharomyces_cerevisiae EF4
>
>  thanks!
>  Sarah
>
> --
> ***********************************************************
> Sarah Djebali - Post-doctoral researcher
> Center for Genomic Regulation (CRG)
> Doctor Aiguader, 88  - 08003 BARCELONA
> Tel. +34 933 160 167 - Fax +34 933 160 099
> sarah.djebali at crg dot es
> http://big.crg.cat/bioinformatics_and_genomics
>
>
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>
> --
> 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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>
>


-- 
***********************************************************
Sarah Djebali - Post-doctoral researcher
Center for Genomic Regulation (CRG)
Doctor Aiguader, 88  - 08003 BARCELONA
Tel. +34 933 160 167 - Fax +34 933 160 099
sarah.djebali at crg dot es
http://big.crg.cat/bioinformatics_and_genomics
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