Good Morning Andrea: the chrUn is unplaced sequence, chromosome unknown:
http://www.hgsc.bcm.tmc.edu/ftp-archive/Btaurus/fasta/Btau20070913-freeze/README.Btau20070913.txt The Ensembl names for these are simply Un without the chr prefix. Beware of cow sequence versions, there are a number of cow genome releases from different assemblies: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \ -e 'select * from dbDb where name like "bos%";' hgcentral --Hiram Andrea Edwards wrote: > Hello all > > Please can you advise me what sequences the ChrUn numbers returned by > liftover refer to. For example a liftover performed on bos taurus from > MD3 to Btau4 returned mappings such as > > chrUn.004.1000 244 245 > > A search in entrez for a sequence 'chrUn.004.1000' or '004.1000' > returns nothing. > > I do not know whether these sequences refer to unlocalized sequences or > unplaced sequences (see definitions below) > > thanks > > Unlocalized sequence: > A sequence found in an assembly that is associated with a specific > chromosome but cannot be ordered or oriented on that chromosome. > > Unplaced sequence: > A sequence found in an assembly that is not associated with any > chromosome. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
