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

[Javier Herrero]

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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