On Wed, Dec 2, 2009 at 2:31 PM, Pratap, Abhishek
<APratap@som.umaryland.edu>wrote:

> Hi All
>
> After taking an exciting BioC course at FredHutch recently, I am trying
> to dive into BioC world to make more sense of NGS data. I would also
> like to thank the entire BioC team present there. You guys were simply
> great. I appreciate you all patiently answering tons of questions and
> taught some of the cool things we can do with BioC packages.
>
> For my current problem I would like to generate coverage plots for a
> small bacterial genome. I have the reads imported as a AlignedRead
> object and I am not sure how to proceed next. The help for the
> "coverage" method didn't get me very far. I am looking for some pointers
> to help me resolve the following questions.
>
> 1. How to create a RLE list from the AlignRead object using coverage
> method ?
> 2. Do I need to pack my reference genome as BSgenome data package in
> order to do this ? If yes I just have the sequence and no group II mask
> file.
> 3. Finally how to plot a RLE list.
>
>
This is a pretty difficult question to answer. Do you want to see all
chromosomes at once (like a karyotype plot)? An overview of entire
chromosomes? Or do you want to explore the data in an interactive genome
browser?

There are many packages in Bioconductor for plotting this sort of data,
including GenomeGraphs and HilbertVis. For genome browsers, there's
rtracklayer and others.

For example, with rtracklayer:
session <- browserSession()
session$coverage <- as(coverage, "RangedData")



> Thanks!
> -Abhi
>
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