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
