[BioC] Any package to calculate NGS coverage and plot it?

[Steve Lianoglou]

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.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

-- 
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