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

[Javier Herrero]

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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>
>
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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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