Hi again ZC, It occurred to me that you are perhaps referring to the scores associated with the 44-way multiple alignment tracks. Here is a description of the fixed step wiggle format used to for phastCons and phyloP data:
http://genome.ucsc.edu/goldenPath/help/phastCons.html Here are some previously-answered questions on the topic: https://lists.soe.ucsc.edu/pipermail/genome/2009-August/019794.html https://lists.soe.ucsc.edu/pipermail/genome/2009-August/019924.html -- Brooke Rhead UCSC Genome Bioinformatics Group Brooke Rhead wrote on 9/22/09 11:40 PM: > Hello ZC, > > To read about the how the 44-way alignments were created, go to the > track details page by clicking on the blue track name in the Genome > Browser (alternatively, follow this link: > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=cons44way). > > The alignments are in MAF format, which is described here: > > http://genome.ucsc.edu/FAQ/FAQformat#format5 > > I hope this information is helpful. If you have further questions, > please feel free to contact us again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > zhuocheng Hou wrote on 9/22/09 5:33 PM: >> Hi All, >> >> Do anyone know how the 44way alignments sequence position generated? For >> example, most alignments have indels, and the original sequence position >> would change after the alignment. So, what's the position in the 44way >> alignment file (wigFix)? >> >> ZC >> _______________________________________________ >> 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
