Hi Jen, This is very helpful. Thanks for the confirmation and suggestions.
Pei On Tue, Apr 27, 2010 at 10:45 PM, Jennifer Jackson <[email protected]> wrote: > 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
