<html><body bgcolor="#FFFFFF"><div>Thanks, that's great!</div><div><br></div><div>Yuan<br><br><br></div><div><br>On 31 Jan 2012, at 09:55, "Kathryn Beal" <<a href="mailto:kbeal@ebi.ac.uk">kbeal@ebi.ac.uk</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>Hi Yuan,<div>I can confirm that these 2 regions look correct in the new release (e66):</div><div>Region 1</div><div><br></div><div><div><font class="Apple-style-span" face="Courier">homo_sapiens/1-1621 TATCTCCATGGGGTCATTTTTTTTCTTTTCTTTCTTTCTCTTTTTCTTTCTTTCTTCTATTTTTTTTTTTTTTTTTTTTTTGAGACAGGATCTTGCTCTG</font></div><div><font class="Apple-style-span" face="Courier">pan_troglodytes/1-1621 TATCTCCATGGGGTCATTTTTTTTCTTTTCTTTCTTTTTCTTTTTCTTTCTTTCTTCTATTTTTTTTTTTTTTTTTTT---GAGACAGGATCTTGCTCTG</font></div><div><font class="Apple-style-span" face="Courier"> ************************************* **************************************** *******************</font></div></div><div><div><font class="Apple-style-span" face="Courier"><br></font></div><div><font class="Apple-style-span" face="Courier">homo_sapiens/1-1621 TCACCCAGGCTGGAGGGCAGTGGGATGATCACTGCTCACTGCAACCCTTCACTTCTCCAAGGCTTAGGTGATCCTCCCATGATGAGGTCAATTTTTAAAG</font></div><div><font class="Apple-style-span" face="Courier">pan_troglodytes/1-1621 TCACCCAGGCTGGAGGGCAGTGGGATGATCACTGCTCACTGAAACC-TTCACTTCTCCAAGGCTTAGGTGATCCTCCCATGATGAGGTCAATTTTTAAAG</font></div><div><font class="Apple-style-span" face="Courier"> ***************************************** **** *****************************************************</font></div></div><div><br></div><div>Region 2</div><div><div><font class="Apple-style-span" face="Courier">homo_sapiens/1-21 TCAAGGGATCCCCAGGCTCAG</font></div><div><font class="Apple-style-span" face="Courier">pan_troglodytes/1-21 TCAAGGGATCCCCAGGCTCAG</font></div><div><font class="Apple-style-span" face="Courier"> *********************</font></div></div><div><br></div><div>Thank you for bringing this to our attention.</div><div>Cheers</div><div>Kathryn<br><div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Thanks Kathryn, it worked when using LASTZ_NET.<br><br>There is slightly problem when I checked for the two regions on release<br>65:<br>region 1: Y:7387430-7387460, given human-chimp alignment :<br><br>Homo sapiens > <span class="Apple-tab-span" style="white-space:pre"> </span>chromosome:GRCh37:Y:7387430:7387460:1<br>Pan troglodytes > <span class="Apple-tab-span" style="white-space:pre"> </span>chromosome:CHIMP2.1.4:Y:24975139:24975169:-1<br><br>Homo sapiens TTGCTCTGTCACCCAGGCTGGAGGGCAGTGG<br>Pan troglodytes CTTGCTCTGTCACCCAGGCTGGAGGGCAGTG<br><br>there is 1 base shift.<br><br>region 2 : Y:13956063-13956083<br><br>Homo sapiens > <span class="Apple-tab-span" style="white-space:pre"> </span>chromosome:GRCh37:Y:13956063:13956083:1<br>Pan troglodytes > <span class="Apple-tab-span" style="white-space:pre"> </span>chromosome:CHIMP2.1.4:1:222316894:222316914:1<br><br>Homo sapiens TCAAGGGATCCCCAGGCTCAG<br>Pan troglodytes GGCTCAAGGGATCCCCAGGCT<br><br>there are 3 bases shift.<br><br>Hope this can be fixed next time.<br><br>yuan<br><br>On Fri, 27 Jan 2012 13:39:07 +0000, Kathryn Beal <<a href="mailto:kbeal@ebi.ac.uk"><a href="mailto:kbeal@ebi.ac.uk">kbeal@ebi.ac.uk</a></a>> wrote:<br><blockquote type="cite">Hi Yuan,<br></blockquote><blockquote type="cite">The human vs chimp alignments in e65 were run using lastz instead of<br></blockquote><blockquote type="cite">blastz and hence the results have a method_link type of LASTZ_NET not<br></blockquote><blockquote type="cite">BLASTZ_NET. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Cheers<br></blockquote><blockquote type="cite">Kathryn<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi ALL,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I am using Ensembl Compara to pull out chimp sequences for<br></blockquote></blockquote>corresponding<br><blockquote type="cite"><blockquote type="cite">human bases, most of them are correct, but for a few of them, I got <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chimp bases that are different from human reference base, but UCSC has<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the same base as human reference base :<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ensembl API version is 63<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">genomedb_name is homo_sapiens<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">genomedb_name is pan_troglodytes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">alignment_type is BLASTZ_NET<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chimp_slices is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">num slice is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">name of the slice is pan_troglodytes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ref_base is G and ref_pos is 2691796 and chimp base is A and chimp_pos<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">is 23773099 and 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chimp_slices is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">num slice is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">name of the slice is pan_troglodytes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ref_base is G and ref_pos is 2750827 and chimp base is T and chimp_pos<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">is 23713497 and 2<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chimp_slices is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">num slice is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">name of the slice is pan_troglodytes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ref_base is A and ref_pos is 2836431 and chimp base is T and chimp_pos<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">is 23626512 and 3<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chimp_slices is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">num slice is 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">.............. <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">When I changed to run ensembl version 65, I got error message :<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-------------------- WARNING ----------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><BLASTZ_NET> and homo_sapiens(GRCh37), pan_troglodytes(CHIMP2.1.4)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 681<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">CALLED BY: svn/modules/AncestralBase.pm LINE: 122<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ensembl API version = 65<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">---------------------------------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-------------------- EXCEPTION --------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">MSG: [] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">STACK<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_Slice_MethodLinkSpeciesSet<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>/nfs/team19/yuan/ensembl-checkout/ensembl-compara-65/modules/Bio/EnsEMBL/Compara/DBSQL/AlignSliceAdaptor.pm:138<br><blockquote type="cite"><blockquote type="cite">STACK AncestralBase::get_ancestral_allele_by_slices_from_db<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/nfs/users/nfs_y/yuan/sanger/src/svn/modules/AncestralBase.pm:135<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">STACK main::get_base_from_pos_file ./get_ancestral_allele.pl:111<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">STACK toplevel ./get_ancestral_allele.pl:51<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ensembl API version = 65<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">---------------------------------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ensembl API version is 65<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">genomedb_name is homo_sapiens<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">genomedb_name is pan_troglodytes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">alignment_type is BLASTZ_NET<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Any idea what went wrong please?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">yuan_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dev mailing list <a 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