[BioC] Amplicon and exon level read counts and GC content

[Yu Chuan Tai]

Hi Sean,

Thanks a lot for your info. I will have a look at your tutorials and try 
it and let you know if I need any help.

Best,
Yu Chuan

On Wed, 30 May 2012, Sean Davis wrote:

> 
> 
> On Wed, May 30, 2012 at 1:17 AM, Yu Chuan Tai <yuchuan at 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
>  
> 
>