<div dir="ltr"><div>The strand should be refer to the local orientation of your slice object relative to the reference genome and not a specific strand of the underlying sequence. <br><br></div>Dan.<br></div><div class="gmail_extra">
<br clear="all"><div><br clear="all"><div>Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)<br>-------------------------------------------------------------------------------------<br><a href="mailto:dsth@cantab.net">dsth@cantab.net</a><br>
<a href="mailto:dsth@cpan.org">dsth@cpan.org</a></div>
</div>
<br><br><div class="gmail_quote">2013/5/2 Bert Overduin <span dir="ltr"><<a href="mailto:bert@ebi.ac.uk" target="_blank">bert@ebi.ac.uk</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello Electra,<div><br></div><div>I don't think this is wrong / a bug as, as far as I know, a slice always encompasses both strands. So, you should do the filtering for features that are located on the forward or reverse strand after retrieving them from the slice.</div>
<div><br></div><div>But maybe I'm wrong .... </div><div><br></div><div>Cheers,</div><div>Bert</div><div><br></div><div><br></div></div><div class="gmail_extra"><div><div class="h5"><br><br><div class="gmail_quote">
On Thu, May 2, 2013 at 4:04 PM, Electra Tapanari <span dir="ltr"><<a href="mailto:et3@sanger.ac.uk" target="_blank">et3@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<br>
Hi all,<br>
<br>
I came across a problem when using the ensembl core API.<br>
<br>
When I am getting a slice where I define chromosome, start, end and<br>
strand and then I get objects from the slice ie,<br>
genes/transcripts/introns etc it returns me objects from both strands.<br>
<br>
<br>
I used this code to test this:<br>
<br>
use strict;<br>
use Gencode::Default;<br>
<br>
<br>
#connect to database<br>
my $db = Gencode::Default->dbconnect("<u></u>ens-livemirror", 3306,<br>
"homo_sapiens_core_71_37", "ensro", undef);<br>
<br>
my $sa = $db->get_SliceAdaptor();<br>
<br>
my $slice=$sa->fetch_by_region('<u></u>chromosome',"3",20000,600000,-<u></u>1) or<br>
die "\n 1.Couldn't get slice\n";<br>
<br>
foreach my $gene (@{$slice->get_all_Genes}){<br>
<br>
$gene=$gene->transform('<u></u>chromosome');<br>
print $gene->stable_id."\t".$gene-><u></u>strand."\n";<br>
<br>
}<br>
<br>
<br>
This is the output:<br>
<br>
ENSG00000223587 1<br>
ENSG00000224918 -1<br>
ENSG00000224318 -1<br>
ENSG00000134121 1<br>
ENSG00000252017 -1<br>
ENSG00000231660 -1<br>
ENSG00000234661 -1<br>
ENSG00000224957 1<br>
<br>
<br>
Isn't this wrong? that it returns me genes from both strands since I am<br>
defining that I am interested in the slice of the negative strand only?<br>
<br>
many thanks in advance,<br>
Electra<br>
<br>
-- <br>
Electra Tapanari<br>
Bioinformatician-Gencode Data Coordinator<br>
Havana Group<br>
Morgan Building<br>
Wellcome Trust Sanger Institute<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridgeshire<br>
CB10 1HH<br>
<br>
E: <a href="mailto:electra.tapanari@sanger.ac.uk" target="_blank">electra.tapanari@sanger.ac.uk</a><br>
T: <a href="tel:%2B44%201223%20496827" value="+441223496827" target="_blank">+44 1223 496827</a><br>
<br>
<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><div><br></div></div></div>-- <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>
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