Hello, Chen. The choice of formats depends upon the assembly quality and phylogenetic distance. Use the following as a guide:
Syntenic net: good quality, small distance Reciprocal best: lower quality, small distance Ordinary net: any quality, any distance You may also want to view the wiki page at http://genomewiki.ucsc.edu/index.php/Mm10_Genome_size_statistics. Though we construct the Syntenic and Reciprocal best files for our own internal use, we don't make those files public. Syntenic nets are easier to produce than Reciprocal best nets. Also, the sequencing coverage for bosTau6 is 9.5X. This can be found in the Assembly Details section of the bosTau6 gateway page: http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Cow&db=bosTau6 Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Tuesday, June 19, 2012 5:45 AM To: [email protected] Subject: [Genome] synNet or reciprocalbest for nomLeu1 , calJac3 and bosTau6 Dear UCSC, I want to do multiple alignment among human(hg19), gibbon(nomLeu1) , marmoset (calJac3) and cow (bosTau6), using multiz. To get a proper whole genome alignment, usually synNet or reciprocalBest pairwise alignment with human is used. Most of the time, you have already given us the alignment files in UCSC(Thanks a lot for that). But for gibbon, marmoset and cow, neither of the two alignment format is given. So which kind of the pairwise alignment method is better for the three species I mentioned above? Plus: The sequencing coverage is 5.6X for gibbon, 6X for marmoset. I don't know the sequencing coverage for cow. Sincerely, Chen Ming _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
