Hello Wei, To clarify, do you not have BLAT matches between the two species or do you have the matches, but it is liftOver that not mapping data? If you don't know, try tweaking liftOver a bit first.
liftOver parameters: - use BED as an input (if you were using positional format) - use -multiple, use -minMatch 0.1 - maybe add in a -minSizeQ 300 (or so) to keep short fragment out (that multiple will capture). Or leave out -minSizeQ, review, then add it back in using a threshold you set based on what type of output you desire. Try the liftOver changes and let us know if this does not solve the problem. If it doesn't, send back details for the processing you (your exact parameters based on the processes from the document) and we can provide feedback for loosening up the match criteria. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/3/10 10:52 AM, Wei Zheng wrote: > Hello, > > I was trying to generate over.chain from S. bayanus to S. cerevisiae > and perform liftOver to map TFBS of S.bayanus to S. cerevisiae > coordinates, using the instructions on > http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/liftOver.txt. > However I can only get less than 10% of my TFBS lifted, the others are > always non-matched. > > I wonder whether you could point out some key parameters in blat, > axtChain, and liftOver steps for such closely related yeast species. > The assembly I used was sacCer1 (16 chromosomes downloaded from UCSC) > for S. cerevisiae and 1098 contigs (downloaded from SGD, reported in > Kellis 2003) for S. bayanus. > > Thank you very much! > > Wei > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
