Hi Mohsen, the pslCDnaFilter program has an option -minId which you could set to 1.00 to remove the non-identical alignments. Does this solve your problem?
cheers Max On Tue, May 31, 2011 at 10:11 PM, Mohsen Sabouri <[email protected]> wrote: > Hi > > For a short sequence (7nt) in human genome assembly, hg19, I want to find the > corresponding 7nt sequence in Mouse assembly mm9, with 100% sequence Identity > to my human 7nt sequence (assuming its 100% conserved). > I am using liftover. For some of my human sequences liftover points to > locations on Mouse that are not 100% identical to my original human sequence. > Is there a parameter in liftover that can be adjusted for this. > > The following example shows the problem. > > content of the inputfile containing one human seq location on hg19: > > chr11 120899760 120899766 pos1 1 + > > the sequence is : CACTTTA > > liftover command line used: > > ./liftOver -minMatch=1 -multiple -minSizeT=7 -minSizeQ=7 -bedPlus=6 > inputfile hg19ToMm9.over.chain outputfile unmapped > > content of the outputfile produced by liftover containing corresponding > conserved mouse coordinates in mm9 assembly is: > > chr9 42275345 42275351 pos1 1 - > > when I plug the new coordinates in the genome browser, mm9, it shows content > of this sequence as: > > TAAGGAG > > which is not 100% match with my original human seq. > > Ideally if there is no 100% identity, then the outputfile should be empty. > > Is there any way to fix this? > > Many thanks! > > > Mohsen Sabouri, PhD > The Scripps Research Institute > 10550 N. Torrey Pines Road > La Jolla, CA 92037 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
