On Wed, May 30, 2012 at 1:17 AM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote:

> Hi,
>
> I have some questions about DNA-Seq and RNA-Seq analyses. In Amplicon
> sequencing, is there any package/function which can extract amplicon-level
> read counts and GC content  from an aligned file of BAM format? The same
> question to exon-level read counts and GC content. More generally, given a
> genomic interval, how could I extract the read count and GC content for
> that interval?
>
>
I wrote a small tutorial that has some of these details in it:

http://watson.nci.nih.gov/~sdavis/tutorials/

See the "Accomplishing Exome Sequencing Data Tasks with Bioconductor"
tutorial.

Sean

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