Hello, This single base is in the middle of a SINE repeat. I expanded the region to 1000 bases (hg18 chr7:69006-70005), ran a web BLAT vs hg19, and came up with strong hits all over the place, including chr7 and chr16.
This is probably just some noise in the data. Repeats are difficult to map. I am a bit surprised that this was able to be mapped at all, but there must be some supporting flanking region that helps to anchor it. If you really want to dig in and figure it out - check out the surrounding region in an even larger scale, run a BLAT, and review the results to understand more about the two regions and why this particular base mapped to a new location. You are moving from an old to a new assembly, which means regions can change, some quite dramatically. This could be the case. Or, more likely, it might just be a repeat bouncing around (although these are possible, they are rare, since we make every attempt to anchor or filter non-specific repeats). You will know what is going on once the data is examined. We hope this helps you learn about how to investigate more on your own and to have some confirmation that this is a perfectly normal part of the dataset (not a problem), Thanks, jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/27/10 11:50 AM, Pei Lin wrote: > Dear Genome Help, > > I was using liftOver to convert a large number of positions in Hg18 to Hg19 > coordinates (Human). It runs great except one position was lifted to a > different chromosome. I tried it on both the cmdline tool and the online > one, the results are the same. > > The trouble position (as input) is > > chr7:69506-69506 > > was lifted to > > chr16:90228418-90228418 > > I choose Human Hg18 to Human Hg19 and left the other selections as default > values. The cmd I used was > > ./liftOver -positions oldfile hg18ToHg19.over.chain newfile unmapped > > I expect the result should be either on the same chromosome or unmapped. > How do you explain this? > > Thanks, > > Pei > > ---------- > Pei Lin > Software Engineer III > Broad Institute > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
