<div dir="ltr">Hi Javier,<br><br>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?<br>
<br>thanks<br>sarah<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 18, 2013 at 3:23 PM, Javier Herrero <span dir="ltr"><<a href="mailto:jherrero@ebi.ac.uk" target="_blank">jherrero@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
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<div><div class="h5"><br>
<br>
<div>On 18/04/13 14:17, Sarah Djebali wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div>
<div>
<div>
<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. <a href="tel:%2B34%20933%20160%20167" value="+34933160167" target="_blank">+34 933 160 167</a> - Fax <a href="tel:%2B34%20933%20160%20099" value="+34933160099" target="_blank">+34 933 160 099</a><br>
sarah.djebali at crg dot es<br>
<a href="http://big.crg.cat/bioinformatics_and_genomics" target="_blank">http://big.crg.cat/bioinformatics_and_genomics</a>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div></div><pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><span class="HOEnZb"><font color="#888888">
</font></span></pre><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
<pre 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>
</font></span></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><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 href="http://big.crg.cat/bioinformatics_and_genomics" target="_blank">http://big.crg.cat/bioinformatics_and_genomics</a>
</div>