Hello Qu, I wanted to add that the Chain and Net files you are looking for can be found here:
ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/vsGalGal3/ ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal3/vsTaeGut1/ They are also available on our downloads page: http://hgdownload.cse.ucsc.edu/downloads.html Best Antonio Coelho UCSC Genome Bioinformatics Group Hiram Clawson wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
