Good Morning Monitha: The hg18 and hg19 assemblies are not identical to each other. They contain different sequence. Please note the tracks on each of the browsers, hg18 has "Hg19 Diff" and hg19 has the track "Hg18 Diff". These tracks indicate the differences between the two assemblies. There are segments of each assembly that do not exist in the other assembly. Some segments are similar but different sequence. Mapping is a one way operation. You can not map back and forth and expect the same result.
--Hiram On 6/5/12 5:03 AM, monithamohan harilkumar wrote: > Hello Sir/Madam, > > I have a doubt reagarding assembly conversion from hg18 and hg19. > The data set which i have is Hg 18, however in order to retrieve nformation > about alle frequencies and something more which is not there in hg 18 i > downloaded all hg19 files of SNP (CommonSNPtable using my java code -sql > connecter) > > My doubt is wheni submitted the hg19 file of chrom,chromstart,chromend, i > recieve a file that is mapped to hg18, but some of them in hg19 are > deleted that is they might not have been there in hg18, its diffcult for me > to maunually check which is deleted or which is not as sometimes there > might be 24 deletions for chrX alone , however I tried remapping this > result of hg18 back to hg19 thinking that i will know which hg19 chrom were > actually mapped but then again i recieve some deletiions , I mean when i > remap it back it must show all that hg19 which was mapped to hg18, then why > is there deletions again > > > Thank You, > MOnitha _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
