Hi Dafil, The following tracks can help you determine if there are any changes between hg18 and hg19, and we also have a track that displays any patches we've included for hg19: "Hg19Diff" track on hg18, and the "Hg18Diff" and "GRC Patch Release" tracks on hg19.
Here is a session for hg19 displaying the 16p12.1 region with the hg19 tracks described above: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Ann&hgS_otherUserSessionName=16p12.1 There is nothing displayed here which means that there are no changes made to that region that you are looking at. However, this doesn't exclude any patches that we may have not incorporated yet. NCBI recently released a patch on January 18th (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml) which could incorporate the region that you are looking at. Also, if after examining the tracks you continue to think there are discrepancies with the human reference assembly, please feel free to report it with NCBI: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ReportAnIssue.shtml Hope this helps you! Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, January 27, 2011 10:48:27 AM Subject: [Genome] Regarding 16p12.1 Hi, We have mapped our short reads against ucsc hg18. We are now summarizing our results. One thing we have to be clear is regarding 16p12.1 region. Recently a paper showed this region has inconsistency in the ref genome build and needs to be flipped due to the inversion of this region, rather than forward orientation. I am wondering is this has been fixed in hg18 build? please let me know. regards, -dafil _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
