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
