[ensembl-dev] gene and exon data download from Illumina (Human BodyMap 2.0)

[Bronwen Aken]

Dear Jerry,

Yes, that is correct: to download the gene and exon coordinates for the Ensembl human Illumina BodyMap data, you will need to query our human RNASeq database using our Perl API.

We do hold regular training courses for users who would like to learn more about our API. (You can contact helpdesk at ensembl.org for more information on these courses.) However, if you would like to try using the Perl API a good starting point is the script that we provided on our blog post:
http://www.ensembl.info/blog/2011/05/24/human-bodymap-2-0-data-from-illumina/
or in cvs:
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-pipeline/scripts/examples/dump_transcripts.pl?root=ensembl&view=co


You will be able to fetch the following gene and exon data using the API:
chromosome
strand
boundary coordinates (start and end)
transcript_length

You will not be able to fetch the following information as it has not been calculated:
raw_count
RPKM


Please let us know if you have any further questions.

Regards,
Bronwen


On 11 Aug 2012, at 00:30, Jerry Li wrote:

> I need to download both gene and exon data from the Ensembl realease 62: RNAseq data from Illumina's Human BodyMap 2.0 project. From what I read, I need to use perl API to access data from the RNA-Seq database homo_sapiens_rnaseq_65_37.
> I am new to perl API and I would appreciate any help with constructing a script in getting the following information for all genes and exons mapping to all 16 tissues:
>  
> For each Exon and Gene (separately)
> chromosome
> strand
> boundary coordinates (start and end)
> raw_count
> transcript_length
> RPKM
>  
> Your help is greatly appreciated!
>  
> -Jerry
>  
> 
>  
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