[ensembl-dev] The number of spanning reads for all genes

[Thibaut Hourlier]

Dear Maartje,
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.

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.
Did you have a look at the perl script on this thread: 
http://lists.ensembl.org/pipermail/dev/2012-September/008071.html. 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.

Regards
Thibaut

On 19/11/12 13:39, J.vandeVorst at gen.umcn.nl wrote:
>
> Hello Ensemble team,
>
> 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.
>
>
> Thank you!
>
> Regards Maartje
>
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
>
> $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
>
>                  -host =>  'ensembldb.ensembl.org',
>
>                  -port =>  5306,
>
>                  -user =>  'anonymous',
>
>                  -dbname =>  'homo_sapiens_core_69_37',
>
> -species => 'Homo_sapiens');
>
> $ga = $db->get_GeneAdaptor();
>
> $gene = $ga->fetch_by_stable_id("ENSG00000109061");
>
> $slice = $gene->slice;
>
> $rnaseqdb = new Bio::EnsEMBL::DBSQL::DBAdaptor(
>
>                  -host =>  'ensembldb.ensembl.org',
>
>                  -port =>  5306,
>
>                  -user =>  'anonymous',
>
>                  -dbname =>  'homo_sapiens_rnaseq_69_37');
>
> $rnaseqsa = $rnaseqdb->get_SliceAdaptor();
>
> $rnaseqslice = $rnaseqsa->fetch_by_name($slice->name);
>
> @transcripts = @{$rnaseqslice->get_all_Transcripts('skeletal_rnaseq')};
>
> foreach my $transcript (@transcripts) {
>
>      foreach my $sf (@{$transcript->get_all_supporting_features()}) {
>
>         #The number of reads that spanned accross the intron
>
>         print STDOUT $sf->hit_name, ' :', $sf->score, "\n";
>
>     }
>
> }
>
>
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>
>
>
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