Hi Perdeep, Sorry for the delayed reply.
"Partially deleted is new" means that the sequence intersects with only part of a single alignment chain in the region. I suspect you have the "Minimum ratio of bases that must remap/Minmatch" setting too high. The online version of liftOver defaults minmatch to .95 for within species liftovers and 0.1 for liftOvers between different species. The command line liftOver application always defaults to 0.95. Thus you may get different results between the two if you don't make sure nimMatch is set the same. Try running the liftOver again at the command line and setting -minMatch=0.1 You can see all liftOver options at the command line by just typing "liftOver". Let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 4/4/11 2:58 PM, Mehta, Perdeep wrote: > Hi, > > I have a couple of files containing several Dog genomic coordinates that I > want to lift over to the Human genome. I have down loaded the > canFam2ToHg19.over.chain files from UCSC website and using it with previously > installed UCSC "liftOver" program to do this. > > For a test, I used just two Dog genome coordinates, as listed below (in file) > chr20 58241270 58241311 contig_1 42 + > chr6 54123651 54123725 contig_2 75 + > > When I use the liftOver program with canFam2ToHg19.over.chain, I get one > mapped to Human genome and second one goes to unmapped output. For example, > This one gets mapped to Human genome (out file 1) > chr1 99175258 99175341 contig_2 1 - > > And the other one remains unmapped (out file 2) > #Partially deleted in new > chr20 58241270 58241311 contig_1 42 + > > When I tested this by using their original sequences the both Dog contigs > actually show corresponding interonic regions of Human genome. First one > mapping to SH3GL2 gene and second to SNX7 gene (this is correctly identified > by liftOver program). > > I do not also understand what "#Partially deleted in new" means? Why is it > not able to lift over the coordinates of the first contig? > > Here are the two sequences used; >> contig_1 > GGCCAGCTCCTGAGTCTGCTGCCCTCTTAGAGCGTAGCCACA >> contig_2 > GGCAGGTCTGGATCTGAATTGAAGCTCTTAATAGCCTAGGAACTAATGTAAAAAGTGGGATGGGATCAGGTATAA > > I will appreciate any help. > > Thanks, > perdeep > > Perdeep K. Mehta, PhD > Research Scientist, Bioinformatics > Research Informatics, Information Sciences Division > St. Jude Children's Research Hospital > > > > ________________________________ > Email Disclaimer: www.stjude.org/emaildisclaimer > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
