<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Jerry,<div><br><div>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.</div><div><br></div><div>We do hold regular training courses for users who would like to learn more about our API. (You can contact <a href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a> 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:</div><div><a href="http://www.ensembl.info/blog/2011/05/24/human-bodymap-2-0-data-from-illumina/">http://www.ensembl.info/blog/2011/05/24/human-bodymap-2-0-data-from-illumina/</a></div><div>or in cvs:</div><div><a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-pipeline/scripts/examples/dump_transcripts.pl?root=ensembl&view=co">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-pipeline/scripts/examples/dump_transcripts.pl?root=ensembl&view=co</a></div><div><br></div><div><br></div><div>You will be able to fetch the following gene and exon data using the API:</div><div><blockquote type="cite"></blockquote>chromosome<br><blockquote type="cite"></blockquote>strand<br>boundary coordinates (start and end)</div><div>transcript_length<br><div><br></div>You will not be able to fetch the following information as it has not been calculated:<br><blockquote type="cite"></blockquote>raw_count<br><blockquote type="cite"></blockquote>RPKM<div><br></div></div><div><div><br></div></div><div>Please let us know if you have any further questions.</div><div><br></div><div>Regards,</div><div>Bronwen</div><div><br></div><div><br><div><div>On 11 Aug 2012, at 00:30, Jerry Li wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>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.</div>
<div>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 <strong>16 tissues</strong>:</div><div> </div><div><u>For each Exon and Gene (separately)</u></div>
<ul><li>chromosome</li><li>strand</li><li>boundary coordinates (start and end)</li><li>raw_count</li><li>transcript_length</li><li>RPKM</li></ul><div> </div><div>Your help is greatly appreciated!</div><div> </div><div>-Jerry</div><p><u></u> </p><div> </div>
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