Hello Joel, Generally lifts should be symmetric but it is not unusual to find some positions that don't lift back . Please see this previously answered mailing list question on this subject:
http://www.soe.ucsc.edu/pipermail/genome/2008-March/015810.html And also note this section from the genomewiki entry it references: "chains should be symmetrical -- e.g. swap human-mouse -> mouse-human chains, and you should get approx. the same chains as if you chain swapped mouse-human blastz alignments. However, Blastz's dynamic masking is asymmetrical, so in practice those results are not exactly symmetrical. Also, dynamic masking in conjunction with changed chunk sizes can cause differences in results from one run to the next." Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Joel McManus wrote: > Hi, > > I have a question about the command line liftover utility. I'm using > liftover to convert the coordinates of several million sequences from > D. melanogaster (2006 release) to D. sechellia. I noticed something > strange in the process. When I liftover from melanogaster to > sechellia, about 12% of these sequences don't liftover. That's not a > big deal to me though, because I can imagine that some of these are in > unmapped regions of D. sechellia. The REALLY weird thing is that when > I take the lifted (mel to sec) coordinates and lift them back into D. > melanogaster coordinates, 2% of these don't lift back. Why is it that > some coordinates that can be mapped from mel to sec, can't be mapped > backwards from sec to mel? How does liftover work? > > If it helps, I'm using a Mac for these operations. > > Thank you for any help with this, > > Joel > > Joel McManus > Postdoctoral Fellow > Graveley Lab > University of Connecticut Health Center > Department of Genetics and Developmental Biology > 263 Farmington Ave > ARB Rm E3053 > Farmington, CT 06030 > phone: 860 679 2092 > [EMAIL PROTECTED] > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
