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

[Sarah Djebali]

Yes, perfect, thanks!
sarah


On Thu, Apr 18, 2013 at 6:21 PM, Javier Herrero <jherrero at ebi.ac.uk> wrote:

>  Hi Michael, Sarah
>
> That is right, C. elegans and S. cereviciae's genomes have no assembly
> gaps.
>
> I guess this answers your query, Sarah.
>
> Kind regards
>
> Javier
>
>
> On 18/04/13 14:58, Michael Paulini wrote:
>
> Hi Sarah,
>
> you will be happy to know that for Caenorhabditis elegans we (WormBase)
> removed the last 4 Ns in 2004 and the last real gaps were filled over a
> decade ago.
> But I cannot speak for other "finished" genome assemblies.
>
> best regards,
>
> Michael
>
> 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
>
>
>
>
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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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