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Dear Maartje,<br>
First I have to warn you that for next release which is due in
January we will update the models of the RNASeq data for human.
These models have been generated with the improved pipeline.<br>
<br>
It is "normal" that you can't get what you want because of the way
we put the data in the database. You will need to use a
DnaAlignFeatureAdaptor.<br>
Did you have a look at the perl script on this thread: <a
href="http://lists.ensembl.org/pipermail/dev/2012-September/008071.html">http://lists.ensembl.org/pipermail/dev/2012-September/008071.html</a>.
It's not exactly what you're trying to do but it is similar and it
shows a way of getting the number of spanning reads. It is stored as
the score of the DnaAlignFeature linked to the exons.<br>
<br>
Regards<br>
Thibaut<br>
<br>
<div class="moz-cite-prefix">On 19/11/12 13:39,
<a class="moz-txt-link-abbreviated" href="mailto:J.vandeVorst@gen.umcn.nl">J.vandeVorst@gen.umcn.nl</a> wrote:<br>
</div>
<blockquote
cite="mid:CE3C1F4B9384554FB57DA18DA78B7E1F2CA081@UMCEXMBX02.umcn.nl"
type="cite">
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<p class="MsoNormal">Hello Ensemble team,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">I was trying to get the
number of spanning reads for one gene by using the API and
the database homo_sapiens_rnaseq_69-37. I used the following
Perl code, but I didn’t get any results. The API version I
use is 69 and I would like to get the number of spanning
reads for all genes. I hope you can help me.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><br>
Thank you!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Regards Maartje<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">use
Bio::EnsEMBL::DBSQL::DBAdaptor;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$db = new
Bio::EnsEMBL::DBSQL::DBAdaptor(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -host
=> 'ensembldb.ensembl.org',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -port
=> 5306,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -user
=> 'anonymous',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -dbname
=> 'homo_sapiens_core_69_37',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">
-species => 'Homo_sapiens');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$ga =
$db->get_GeneAdaptor();<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$gene =
$ga->fetch_by_stable_id("ENSG00000109061");<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$slice =
$gene->slice;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$rnaseqdb = new
Bio::EnsEMBL::DBSQL::DBAdaptor(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -host
=> 'ensembldb.ensembl.org',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -port
=> 5306,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -user
=> 'anonymous',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> -dbname
=> 'homo_sapiens_rnaseq_69_37');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$rnaseqsa =
$rnaseqdb->get_SliceAdaptor();<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$rnaseqslice =
$rnaseqsa->fetch_by_name($slice->name);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">@transcripts =
@{$rnaseqslice->get_all_Transcripts('skeletal_rnaseq')};<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">foreach my $transcript
(@transcripts) {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> foreach my $sf
(@{$transcript->get_all_supporting_features()}) {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> #The number of
reads that spanned accross the intron<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> print STDOUT
$sf->hit_name, ' :', $sf->score, "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> }<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">}<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br clear="all">
<p style="font-size:13px;font-family:arial;"> Het UMC St Radboud
staat geregistreerd bij de Kamer van Koophandel in het
handelsregister onder nummer 41055629.<br>
The Radboud University Nijmegen Medical Centre is listed in the
Commercial Register of the Chamber of Commerce under file number
41055629.<br>
</p>
<br>
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<br>
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