Dear Hiram Thank you for your clarification.
With best wishes Qasim --- Qasim Ayub Team 19: Human Evolution Room Number E2-18 The Sulston Laboratories The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA United Kingdom E-mail: [email protected] Tel: +44-(0)-1223-834244 Ext:7652 Fax: +44-(0)-1223-494919 -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: 02 December 2011 20:11 To: Qasim Ayub Cc: [email protected] Subject: Re: [Genome] Y chromosome coordinates Good Afternoon Qasim: Please note the Hg18 Diff and Hg19 Diff tracks on the UCSC genome browser assemblies hg19 and hg18 respectively. These tracks indicate the assembly differences between the two assembly. Your mentioned region on hg18 chrY:12,838,588-13,879,980 can be seen in this session with the Hg19 Diff track turned on: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=hg18.chrY.changeHg19 UCSC translates these coordinates to hg19 as: chrY:14,328,588-15,370,586 seen in this session: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=hg19.chrY.changeHg18 Note that about half of this region is assembled with different contig contents. There may be differences in the gene annotations on the two genomes due to the different contig sequences used in the assembly. --Hiram Qasim Ayub wrote: > Hi > > > > I am trying to map Y chromosomal coordinates from build hg18 to hg19. > Last week when I used the Lift Genome Annotations Tool using the > NCBIBuild36 coordinates (chrY:12838588-13879980), I obtained the GRCh37 > Coordinates (chrY:14328588-15370586) but now I get a message indicating > "Split in new". > > When I check in Ensembl it gives the following message: > > This data includes 10 gaps where the input coordinates could not be > mapped directly to the output assembly. > > Y Ensembl .sdf 14726405 15370586 > - . > > Y Ensembl .sdf 14716432 14725776 > - . > > Y Ensembl .sdf 13226453 13226453 > - . > > Y Ensembl .sdf 14709281 14716431 > - . > > Y Ensembl .sdf 13219301 13219301 > - . > > Y Ensembl .sdf 14664254 14709280 > - . > > Y Ensembl .sdf 13174273 13174273 > - . > > Y Ensembl .sdf 14661473 14664253 > - . > > Y Ensembl .sdf 13171483 13171491 > - . > > > > The region is a well behaved single copy X degenerate region that was > sequenced from, if I recall correctly, BAC clones from a single > individual. I was unable to find any reference to a recent change in the > Y annotation and was wondering if you could assist in trying to > ascertain what may have happened. > > With best wishes > > Qasim > --- > Qasim Ayub > Team 19: Human Evolution > Room Number E2-18 > The Sulston Laboratories > The Wellcome Trust Sanger Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge CB10 1SA > United Kingdom > > E-mail: [email protected] > Tel: +44-(0)-1223-834244 Ext:7652 > Fax: +44-(0)-1223-494919 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
