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Hi Sarah<br>
<br>
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.<br>
<br>
Javier<br>
<br>
<div class="moz-cite-prefix">On 18/04/13 14:17, Sarah Djebali wrote:<br>
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<div>Dear developpers,<br>
<br>
</div>
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?<br>
<br>
</div>
I would need in particular the gaps for:<br>
- Caenorhabditis_elegans WBcel215<br>
- Caenorhabditis_elegans WS220 <br>
- Saccharomyces_cerevisiae EF2<br>
- Saccharomyces_cerevisiae EF3<br>
- Saccharomyces_cerevisiae EF4 <br>
<br>
</div>
thanks!<br>
</div>
Sarah<br clear="all">
<div><br>
-- <br>
***********************************************************<br>
Sarah Djebali - Post-doctoral researcher<br>
Center for Genomic Regulation (CRG)<br>
Doctor Aiguader, 88 - 08003 BARCELONA<br>
Tel. +34 933 160 167 - Fax +34 933 160 099<br>
sarah.djebali at crg dot es<br>
<a moz-do-not-send="true"
href="http://big.crg.cat/bioinformatics_and_genomics"
target="_blank">http://big.crg.cat/bioinformatics_and_genomics</a>
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<br>
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<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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