Thank you, Dan.<div><br></div><div>You mentioned that you no longer build on low coverage genomes in Ensembl, what do you guys do with the short reads (such as Illumina GA II/Hiseq) assembled genomes? So far as I know the Atlantic Cod genome which was published last summer in Nature was built based on the projection genebuild.<br>
<br>Best Reguards<br><br><div class="gmail_quote">On Wed, Apr 18, 2012 at 4:43 PM, Dan Barrell <span dir="ltr"><<a href="mailto:db8@sanger.ac.uk">db8@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">
<div bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
The document low_coverage_gene_build.txt is quite old and possibly
very out of date as we no longer build on low coverage genomes in
Ensembl. As far as I know, the reason that the semantics of the
reference and target terms got swapped is to do with the importance
of directionality in a Net. When dealing with the low coverage
genomes the idea was that they wanted the species they were
projecting onto as the reference because it is important that each
bp in the target species aligns to at most one location in the
reference species. <br>
<br>
I would suggest you also look at the Ensembl Compara documentation
which is maintained here:<br>
<br>
ensembl-compara/docs/README-low-coverage-genome-aligner<br>
<br>
Dan<div><div class="h5"><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 17/04/12 12:47, Zhang Di wrote:
</div></div><blockquote type="cite"><div><div class="h5">Hi,
<div><br>
</div>
<div>I'm using ensembl pipeline for projection genebuild.</div>
<div><br>
</div>
<div>when I read the doc low_coverage_gene_build.txt, I was
confused by the target/query genome terms.</div>
<div><br>
</div>
<div>It calls our newly sequenced genome the target, calls the
reference genome the query.</div>
<div><br>
</div>
<div>It is contrary to lastz terms where target means reference
and query means our sequences.</div>
<div><br>
</div>
<div>It just OK if I stick to this convention.</div>
<div><br>
</div>
<div>However,</div>
<div><br>
</div>
<div>In the whole genome alignment section in the same doc,</div>
<div><br>
</div>
<div>It says that :</div>
<div><br>
</div>
<div> "each bp in the target genome should be represented at
most once."</div>
<div><br>
</div>
<div>What does it mean by saying "target"?</div>
<div><br>
</div>
<div>lastz-chain-net produces the lastz termed "target genome"
with this property.</div>
<div><br>
</div>
<div>Does it mean that I should set my genome as the reference
genome, while the genome from ensembl such as "human" as the
non-reference in the compara/hive pipeline?</div>
<div><br>
</div>
<div>I can project human genes to my genome with this somewhat
weird setting, in the next wga2genes step?</div>
<div><br>
</div>
<div>Some slice of human genome containing genes may exist several
times in the compara_db, how can it produce gene projection
right here?</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Best Reguards</div>
<div><br>
</div>
<div>-- <br>
Zhang Di<br>
</div>
<br>
<fieldset></fieldset>
<br>
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</blockquote>
<br>
<br>
</div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Zhang Di<br>
</div>