<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Javier is right, you can use top-level. I thought it might return more than the advertised 22 unplaced, but I might be just looking at the wrong query.<div><br></div><div><div><font class="Apple-style-span" face="Courier">mysql> select coord_system.name, coord_system_id, count(*) from seq_region inner join seq_region_attrib using (seq_region_id) inner join coord_system using (coord_system_id) where attrib_type_id = 6 group by coord_system_id;</font></div><div><font class="Apple-style-span" face="Courier">+------------+-----------------+----------+</font></div><div><font class="Apple-style-span" face="Courier">| name | coord_system_id | count(*) |</font></div><div><font class="Apple-style-span" face="Courier">+------------+-----------------+----------+</font></div><div><font class="Apple-style-span" face="Courier">| scaffold | 2 | 44 | </font></div><div><font class="Apple-style-span" face="Courier">| chromosome | 3 | 22 | </font></div><div><font class="Apple-style-span" face="Courier">+------------+-----------------+----------+</font></div><div><font class="Apple-style-span" face="Courier">2 rows in set (0.00 sec)</font></div></div><div><br></div><div><br></div><div>All the best,</div><div><br></div><div>Will<br><div><div><br></div><div><br><div><br></div><div><br></div><div><br><div><div>On 4 Sep 2012, at 15:11, Javier Herrero wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Sergei<br><br>You can use<br><br>my @slices = @{ $slice_adaptor->fetch_all('toplevel') };<br><br>instead. The coordinate system alias "toplevel" corresponds to all the so-called top-level sequences, i.e. the chromosomes (if any) and all the unplaced scaffolds.<br><br>I hope this helps<br><br>Javier<br><br>On 01/09/12 07:58, Sergei Manakov wrote:<br><blockquote type="cite">Hello,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">According to GRCm38 description there are 21 chromosomes and 22<br></blockquote><blockquote type="cite">unplaced scaffolds this version of the mouse genome.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">How can I get slices for these unplaced scaffolds?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">this doesn't work:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">my @slices = @{ $slice_adaptor->fetch_all('chromosome') };<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">thanks very much!<br></blockquote><blockquote type="cite">Sergei<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br>-- <br>Javier Herrero, PhD<br>Ensembl Coordinator and Ensembl Compara Project Leader<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge - CB10 1SD - UK<br><br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></div></div></div></body></html>