Hello, Not every base position has a value attribute. Therefore, there is not one line for every base on the chromosome.
To navigate the file, search for lines similar to the header line. As an example, these are the first 10 "header" or "navigation" lines within the file chr19.phyloP44way.primate.wigFix: &grep fix *Fix | head fixedStep chrom=chr19 start=11001 step=1 (actual first line) fixedStep chrom=chr19 start=13449 step=1 fixedStep chrom=chr19 start=26654 step=1 fixedStep chrom=chr19 start=91295 step=1 fixedStep chrom=chr19 start=114543 step=1 fixedStep chrom=chr19 start=134039 step=1 fixedStep chrom=chr19 start=136621 step=1 fixedStep chrom=chr19 start=156093 step=1 fixedStep chrom=chr19 start=191898 step=1 fixedStep chrom=chr19 start=204220 step=1 The gaps between the base proceeding a navigation line and the next start base do not have attribute values. Then, where more conservation data is available, the step=1 continues. Hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "zhuocheng Hou" <[email protected]> wrote: > From: "zhuocheng Hou" <[email protected]> > To: [email protected] > Sent: Monday, August 31, 2009 1:39:01 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] not complete list of genome alignment/conservation file? > > Hi Everyone, > > I downloaded the 44_way phastCon conservation score files(i.e., > chr19.phastCons44way.primates.wigFix) and want to retreive the > conservation > score for each base. However, I found the inconsistant file between > genome > brower and downloaded file. I don't know what's going on. Can anyone > give me > some ideas about these wigFix file? > > Data examples: > > If we input chr19:59865391- 59873622 into the genome browser for > human, we > can get mammCon score for each base. However, if we want to directly > get > these scores from the wigFix file, we cannot get these values because > the > longest bases (54282264) didn't mathc the input values. It seems > wigFix file > cannot provide all the base conservation score, but how the genome > brower > get these conservation score? > > Thanks, > 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
