[ensembl-dev] mRNA abundance per exon question

[Jerry Li]

Dear Thibaut and Ensembl dev community,
    My sincere gratitute for your help.  I took your advice and now I'm
able to map RNAseq gene ids to EntrezGene ids.

I need to ask one more big favor from you.  Has any of you tried retrieving
mRNA abundance information on a per Exon or per Transcript basis from
RNAseq?  I have read through the Ensembl API Core documentation and
tutorial but still have no clue on how to do it.

Your help is greatly appreciated!!!

Jerry


On Thu, Aug 30, 2012 at 3:50 AM, th3 <th3 at sanger.ac.uk> wrote:

> Hi Jerry,
>
> We only get external reference (xref) like the EntrezGene ID for the core
> databases.
> So for every gene from the rnaseq database you need to get the gene from
> core that overlaps your rnaseq gene and then you can check if they have an
> xref of your choice.
>
> # You will need a GeneAdaptor on your core DB
> $coredbga = $coredb->get_GeneAdaptor;
> # You will need a SliceAdaptor on your core DB
> $coredbsa = $coredb->get_SliceAdaptor;
>
> foreach my $slice (@$slices) {
>   # fetch genes from rnaseq
>   my $genes = $slice->get_all_Genes($logic_**name);
>   foreach my $gene (@$genes) {
>     $coreslice = $coresa->fetch_by_name($gene->**feature_Slice()->name);
>     foreach my $cgene (@{$coredbga->fetch_all_by_**
> Slice_and_external_dbname_**link($coreslice, undef, undef,
> "EntrezGene")}) {
>       foreach my $dbes ($cgene->get_all_DBLinks("**EntrezGene")){
>
>         foreach my $dbe (@{$dbes}){
>           print $dbe->primary_id(), "\t";
>         }
>       }
>     }
>   }
> }
>
> Hope this helps
>
> Thibaut
>
>
> On 2012-08-30 04:24, Jerry Li wrote:
>
>> Hi All,
>> Sorry to bother you all on this topic but I can really use some
>> advice.
>>
>> Based on an example I found in the email archive
>> http://lists.ensembl.org/**pipermail/dev/2010-September/**005130.html<http://lists.ensembl.org/pipermail/dev/2010-September/005130.html>[1]
>>
>> I put together the following code to retrieve the EntrezGene IDs based
>> on Ensembl $gene.  However, no result was returned.
>> The database I accessed was homo_sapiens_rnaseq_68_37, and logic_name
>> is ovary_rnaseq.
>> Can anyone provide some pointer on how I can get this data?
>>
>> foreach my $slice (@$slices) {
>>   # fetch genes from rnaseq
>>   my $genes = $slice->get_all_Genes($logic_**name);
>>   foreach my $gene (@$genes) {
>>         foreach my $dbes ($gene->get_all_DBLinks("**EntrezGene")){
>>             foreach my $dbe (@{$dbes}){
>>                 print $dbe->primary_id(), "t";
>>             }
>>         }
>>     }
>> }
>>
>>
>> Thanks,
>> Jerry
>>
>>
>> Links:
>> ------
>> [1] http://lists.ensembl.org/**pipermail/dev/2010-September/**005130.html<http://lists.ensembl.org/pipermail/dev/2010-September/005130.html>
>>
>
>
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