Hi David, > 1. are the snps recorded in the 'Genome Variants' lines all the snps > that were reported in the genomes of venter and watson?
For Watson yes, but not for Venter. A bit more information about the variants that we show is available on the item details pages that appear when you click on an item in the genome browser. Scroll down to the "Methods" section, where you will find a brief description of how the variants were obtained, and links to more info. For Venter, the file ftp://ftp.jcvi.org/pub/data/huref/HuRef.InternalHuRef-NCBI.gff was downloaded, but only the lines ending with Method1 (variant was kept in its original form and not post-processed) and without N as an allele were kept for display. For Watson, the file ftp://ftp.hapmap.org/hapmap/jimwatsonsequence/watson_snp.gff.gz was downloaded and all SNPs in the file were kept. Belinda Giardine at PSU translated the info into those files into database tables for UCSC to display, and might have more to say about the filtering of SNPs. > 2. were all genomic regions covered by these analyses? i.e., if I dont > see any snp does it mean that there are none, or could it be that the > particular region has not been analyzed? If the latter is the case, > where do I find the information what has been covered by the variant > analysis and what was not covered by it? The information available for each genome varies. We have not computed depth of coverage to accompany the SNPs, and for some genomes I'm not sure whether sufficient info is available. For Venter, read depth coverage along h6 assembly scaffolds is available (see ftp://ftp.jcvi.org/pub/data/huref/README_scaffold_depth), and there might be a way to link that to NCBI 36 coords using other files in ftp://ftp.jcvi.org/pub/data/huref/ , but it looks like it would be non-trivial (I'm guessing one would have to reconstruct the h6 scaffold sequences from reads, align those to NCBI 36, and then translate the scaffold depth encodings into NCBI 36 coords). For Watson, the file ftp://ftp.hapmap.org/hapmap/jimwatsonsequence/watson-blocks.gz contains reference genome coordinates of aligned reads, so depth of coverage along the genome could be deduced from that. > 3. do you have a tool that can count the number of individual snps in > a given range over some region of the chromosome? Yes, our Table Browser tool can do that. Click on the Tables link at the top of the genome browser page. Then select "Variation and Repeats" as the group, "Genome Variants" as the track, and either pgVenter or pgWatson as the table. Set the region to position and enter the coordinates of your region. Then click the "summary/statistics" button at the bottom of the form. The first statistic reported is item count. > 4. where do I find the information of CNVs, inversions and deletions > of larger sections than single snps in the individual Genome Variants? I would look in the download directories where we got the SNPs: ftp://ftp.jcvi.org/pub/data/huref/ for Venter and ftp://ftp.hapmap.org/hapmap/jimwatsonsequence/ for Watson. I don't see anything other than SNPs for Watson, but there is a README_for_variants.Homozygous_Indels_Inversion.txt and HuRef.homozygous_indels_inversion.061109.gff for Venter. You might also want to contact the authors of the publications (see the Reference section at the end of the item details page). I hope that helps, and if you have any more questions, please send them to us at [email protected]. Angie ----- [email protected] wrote: > From: [email protected] > To: [email protected] > Sent: Monday, October 5, 2009 11:19:02 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] help with individual genome variants > > I need some advice concerning your genome browser and I hope you can > help me get the relevant information. > > Trying out some theoretical model concerning inverted repeats, that > has been developed using your assemblies (hg18 and hg19), we wish to > see whether indvidual genomic sequences (e.g. venter and watson), > abide by it. > Using your browser I can observe the snps found on these Genome > Variants but I am left with some questions that bother me: > > 1. are the snps recorded in the 'Genome Variants' lines all the snps > that were reported in the genomes of venter and watson? > > 2. were all genomic regions covered by these analyses? i.e., if I dont > see any snp does it mean that there are none, or could it be that the > particular region has not been analyzed? If the latter is the case, > where do I find the information what has been covered by the variant > analysis and what was not covered by it? > > 3. do you have a tool that can count the number of individual snps in > a given range over some region of the chromosome? > > 4. where do I find the information of CNVs, inversions and deletions > of larger sections than single snps in the individual Genome Variants? > > > Your help will be much appreciated. > > Many thanks, > > David Horn > http://horn.tau.ac.il > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
