Good Morning Qu: Please examine a typical sequence of instructions in the source tree file: src/hg/makeDb/doc/calJac3.txt
This is merely an example. Your exact sequence will be different. We use syntenic best pair-wise alignments when the two genomes have large N50 sizes for their chromosomes (== well assembled genomes) We use reciprocal best pair-wise alignments when one of the genomes has a small N50 size of its scaffolds or contigs. --Hiram Qu Zhang wrote: > Hi UCSC help group, > > I'm trying to align the chicken, zebra finch and lizard genomes by > multiz-tba, since all the possible pairwise alignments have been done by > UCSC, I'm wondering which files I need to continue multiz alignment step, > the chain file or the net file? Also, how could I converse chain/net files > to MAF files as the multiz input? > > Another minor question is there is zebra finch to chicken chain and net data > from table browser, but I didn't see that on the ftp site, is it only > possible to download these files from table browser? > > Any help would be appreciated! > > Best, > Qu > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
