Dear list, I have some NGS sequences that enriched in different regions along the genome. I want to calculate the coverage of the short sequences and plot the sequences in a specific region. To plot, I just want a function to simply plot the tags and chromosome (it is OK if also plot the gene there), but not other things like in genome browser. Is there any package can do this? Thank you! Best, Xiaohui

On 05/28/2011 06:24 AM, Steve Lianoglou wrote: > Hi, > > On Fri, May 27, 2011 at 9:24 PM, Xiaohui Wu<wux3 at="" muohio.edu=""> wrote: >> Dear list, >> >> I have some NGS sequences that enriched in different regions along >> the genome. I want to calculate the coverage of the short sequences >> and plot the sequences in a specific region. To plot, I just want >> a function to simply plot the tags and chromosome (it is OK if also >> plot the gene there), but not other things like in genome browser. >> Is there any package can do this? A simple approach is to calculate coverage library(GenomicRanges) aln = readGappedAlignments(<bamfile>) cvg = coverage(aln) then slice to find views onto islands isles = slice(cvg, <min-depth>) or view selected coordinates v = Views(cvg, <interesting-granges>) then visualize as a simple 'skyline', e.g., plot(as.integer(isles[[1]])) or as a 'movie' for (i in seq_len(length(isles))) plot(as.integer(isles[[i]]), type="l") None of this tested, so hopefully not too misleading. Martin > > You can try GenomeGraphs as a start: > http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs. html > > With a bit of work I reckon you can get what you want. Read through > the vignette -- last I remember there was an NGS example there. > > I don't imagine you'll get very good results when you try to plot an > entire genome, so you'll have to identify your regions of interest > first and plot them individually (using slice() over your coverage > vector would be an easy first-attempt to find them). > > -steve > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Hi, On Fri, May 27, 2011 at 9:24 PM, Xiaohui Wu <wux3 at="" muohio.edu=""> wrote: > Dear list, > > I have some NGS sequences that enriched in different regions along the genome. I want to calculate the coverage of the short sequences and plot the sequences ?in a specific region. To plot, I just want a function to simply plot the tags and chromosome (it is OK if also plot the gene there), but not other things like in genome browser. Is there any package can do this? You can try GenomeGraphs as a start: http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs.ht ml With a bit of work I reckon you can get what you want. Read through the vignette -- last I remember there was an NGS example there. I don't imagine you'll get very good results when you try to plot an entire genome, so you'll have to identify your regions of interest first and plot them individually (using slice() over your coverage vector would be an easy first-attempt to find them). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Thanks, Martin and Steve. I'll use GenomicRanges to calculate coverage, and GenomeGraphs to plot my data. Xiaohui ------------------------------------------------------------- Martin Morgan 2011-05-28 23:37:22 Steve Lianoglou Wu, Xiaohui Ms.; bioconductor at r-project.org Re: [BioC] Any package to calculate NGS coverage and plot it? On 05/28/2011 06:24 AM, Steve Lianoglou wrote: > Hi, > > On Fri, May 27, 2011 at 9:24 PM, Xiaohui Wu<wux3 at="" muohio.edu=""> wrote: >> Dear list, >> >> I have some NGS sequences that enriched in different regions along >> the genome. I want to calculate the coverage of the short sequences >> and plot the sequences in a specific region. To plot, I just want >> a function to simply plot the tags and chromosome (it is OK if also >> plot the gene there), but not other things like in genome browser. >> Is there any package can do this? A simple approach is to calculate coverage library(GenomicRanges) aln = readGappedAlignments(<bamfile>) cvg = coverage(aln) then slice to find views onto islands isles = slice(cvg, <min-depth>) or view selected coordinates v = Views(cvg, <interesting-granges>) then visualize as a simple 'skyline', e.g., plot(as.integer(isles[[1]])) or as a 'movie' for (i in seq_len(length(isles))) plot(as.integer(isles[[i]]), type="l") None of this tested, so hopefully not too misleading. Martin > > You can try GenomeGraphs as a start: > http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs. html > > With a bit of work I reckon you can get what you want. Read through > the vignette -- last I remember there was an NGS example there. > > I don't imagine you'll get very good results when you try to plot an > entire genome, so you'll have to identify your regions of interest > first and plot them individually (using slice() over your coverage > vector would be an easy first-attempt to find them). > > -steve > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 .