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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>
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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>
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