Hi Andrea,<div><br></div><div>I suspect that your BioMart results are truncated because the query is too large.<div><br></div><div>However, that doesn't explain your API results .... How does your API code look like?<br>
<div><br></div><div>Cheers,</div><div>Bert<br><br><div class="gmail_quote">On Fri, May 6, 2011 at 3:45 PM, Andrea Edwards <span dir="ltr"><<a href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello<br>
<br>
I'm sorry for the basic question but I was looking at the ensembl core schema and trying to retrieve just the exons on chromosomes and couldn't work out why i am getting such different figures than with biomart and the perl api<br>

<br>
For example for cow there are 25670 exons in genes with biomart and the api but with this sql  ~210k exons. This code is just looking for exons on chromosomes 1-30 and X<br>
<br>
select count(distinct stable_id) from exon e inner join exon_stable_id es using(exon_id) inner join seq_region sr using(seq_region_id) where sr.coord_system_id = 2 and <a href="http://sr.name" target="_blank">sr.name</a> REGEXP '^[1-9]|^X'  and e.is_current=1<br>

<br>
I get 8k just on chromosome 1<br>
<br>
I'm sure this is simple and perhaps its because its Friday afternoon but I'm just not seeing it!!<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>United Kingdom<br>
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