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
