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    Hi Zhang<br>
    <br>
    In the PAIR_ALIGNER module, the reference_collection_name
    corresponds to the target_collection_name. In the other two modules
    (CHAIN_CONFIG and NET_CONFIG), the reference_collection_name
    corresponds to the query_collection_name. Part of the reason to
    change the name was to be able to use the same name for all 3
    modules.<br>
    <br>
    In short, just use the same genome as the reference_collection_name
    for all 3.<br>
    <br>
    Note that we have changed the way we run this pipeline and this
    configuration file is not longer supported. The documentation for
    the new pipeline is available under
    ensembl-compara/docs/README-pairaliger. Obviously, you can still use
    ensembl_64 API and pipeline for as long as you want.<br>
    <br>
    I hope this helps<br>
    <br>
    Javier<br>
    <br>
    On 18/04/12 13:33, Zhang Di wrote:
    <blockquote
cite="mid:CAMHeD-cCz9zoQ9CHKMi799xWxR-2b1WxWEHpeWpW=NEDUNhCNw@mail.gmail.com"
      type="cite">Thank you, Javier
      <div><br>
      </div>
      <div>You mean I should set some thing like below in the
        compara_2x.conf to prepare the compara_db for gene projection.</div>
      <div><br>
      </div>
      <blockquote style="margin:0 0 0 40px;border:none;padding:0px">
        <div>{</div>
        <div>TYPE => PAIR_ALIGNER,</div>
        <div>reference_collection_name => 'human',</div>
        <div>non_reference_collection_name => 'my_genome',</div>
        <div>}</div>
        <div>
          <div>{</div>
        </div>
        <div>
          <div>TYPE => CHAIN_CONFIG,</div>
        </div>
        <div>
          <div>non_reference_collection_name => 'human',</div>
        </div>
        <div>
          <div>reference_collection_name => 'my_genome',</div>
        </div>
        <div>
          <div>}</div>
        </div>
        <div>
          <div>{</div>
        </div>
        <div>
          <div>TYPE => NET_CONFIG,</div>
        </div>
        <div>
          <div>non_reference_collection_name => 'human',</div>
        </div>
        <div>
          <div>reference_collection_name => 'my_genome',</div>
        </div>
        <div>
          <div>}</div>
        </div>
        <div><br>
        </div>
      </blockquote>
      <div>By the way, I'm using ensembl-compara version 64.</div>
      <div><br>
        <div class="gmail_quote">On Wed, Apr 18, 2012 at 4:57 PM, Javier
          Herrero <span dir="ltr"><<a moz-do-not-send="true"
              href="mailto:jherrero@ebi.ac.uk">jherrero@ebi.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"> Dear Zhang<br>
              <br>
              The query/target naming has always been quite confusing in
              the pairwise alignment pipeline. When running an
              alignment, you use a sequence (query) to look for similar
              regions in another sequence (target genome). The pairwise
              alignment pipeline has three major steps: (a) raw
              alignments; (b) chaining; and (c) netting. The chaining
              step tries to link all the raw alignments that are in the
              same order and orientation to create a longer structure
              called chain. The netting step requires you to define a
              target genome such as the so-called nets are the subset of
              chains that form the best-in-genome alignment. In other
              words, the final set will provide you for each bp of the
              target genome with the best match on the other genome.<br>
              <br>
              As I said earlier, query and target are often times
              confusing terms. To make the situation worse, we use to
              run the pipeline such as the query for the raw alignment
              step was the target for the chaining and netting steps and
              vice versa. We have now changed the way we refer to both
              sequences and call them reference and non-reference
              genomes. We find that nomenclature less confusing.<br>
              <br>
              Kind regards<br>
              <br>
              Javier
              <div>
                <div class="h5"><br>
                  <br>
                  On 18/04/12 09:43, Dan Barrell wrote:
                  <blockquote type="cite"> 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<br>
                    <br>
                    <br>
                    <br>
                    <br>
                    <br>
                    <br>
                    <br>
                    <br>
                    <br>
                    On 17/04/12 12:47, Zhang Di wrote:
                    <blockquote type="cite">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>
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</pre>
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                  </blockquote>
                  <br>
                </div>
              </div>
              <span class="HOEnZb"><font color="#888888">
                  <pre cols="72">-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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        </div>
        <br>
        <br clear="all">
        <div><br>
        </div>
        -- <br>
        Zhang Di<br>
      </div>
      <br>
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      <br>
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    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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