[ensembl-dev] mRNA abundance per exon question

[Bronwen Aken]

Hi Jerry,

Up to now, our main effort with RNAseq has been focussed around gene annotation. We have developed a method where we can annotate protein-coding gene models from RNAseq data. This method includes a step where we annotate introns and count the number of reads that span each intron. The intron features are stored as dna_align_features and their score column contains a count of the number of reads that support the intron. 

The counts are also visible on our website. In the example below, we have the human MYOG gene. If you click the grey boxes for Breast intron-spanning reads and Skeletal muscle intron-spanning reads, you can see in the Read Coverage line that more reads support the skeletal muscle (51) than breast tissue (9).



In the future we would like to provide users with an expression level but we have not yet looked into this yet.

Cheers,
Bronwen


On 31 Aug 2012, at 02:15, Jerry Li wrote:

> 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 [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
> 
> 
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