[BioC] base-specific read counts

[Martin Morgan]

On 06/06/2012 10:43 PM, Yu Chuan Tai wrote:
> Hi,
>
> Is there any way to calculate base-specific read counts for a given
> genomic interval (including 1-base interval), for paired-end data
> aligned by Bowtie2 in BAM format?

Thanks for posting to the Boic mailing list! Functions like 
readGappedAlignments, scanBam, etc. take an argument ScanBamParam that 
in turn has an argument 'which' to specify, using GRanges, the regions 
of a bam file you want to query

   gwhich <- GRanges("chr1", IRanges(c(1000, 2000, 3000), width=100)),
       c("+", "+", "-"))
   param <- ScanBamParam(which=gwhich)
   scanBam("my.bam", param=param)

Base-level coverage is also available with ?applyPileups, see 
example(applyPileups).

Martin

> Thanks!
>
> Best,
> Yu Chuan
>
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