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

[Michael Love]

hi Yu Chuan, 

I wrote two convenience functions, countBamInGRanges and getGCcontent, for the 
exomeCopy package for these tasks.  You can take a look at the first part of th
e vignette here:

[1]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 [2]<yuchuan at stat.berkeley.edu>
To: [3]bioconductor at r-project.org
Subject: [BioC] Amplicon and exon level read counts and GC content
Message-ID: [4]<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

References

   1. http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html
   2. mailto:yuchuan at stat.berkeley.edu
   3. mailto:bioconductor at r-project.org
   4. mailto:alpine.DEB.2.00.1205292216070.8774 at arwen.Berkeley.EDU