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

Yu Chuan Tai yuchuan at stat.berkeley.edu
Wed May 30 21:31:21 CEST 2012

Hi Michael,

Thanks for the info....looks like these functions are what I need. I will 
check your package out and let you know if I have any question.

Yu Chuan

On Wed, 30 May 2012, Michael Love wrote:

> hi Yu Chuan, 
> I wrote two convenience functions, countBamInGRanges and getGCcontent, for the exomeCopy package for these tasks.  You c
> an take a look at the first part of the vignette here:
> http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html
> best,
> Mike
> Date: Tue, 29 May 2012 22:17:29 -0700 (PDT)
> From: Yu Chuan Tai <yuchuan at stat.berkeley.edu>
> To: bioconductor at r-project.org
> Subject: [BioC] Amplicon and exon level read counts and GC content
> Message-ID: <alpine.DEB.2.00.1205292216070.8774 at arwen.Berkeley.EDU>
> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
> 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?
> Thanks for any input!
> Best,
> Yu Chuan

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