[BioC] base-specific read counts

[Sean Davis]

On Thu, Jun 7, 2012 at 11:03 AM, Yu Chuan Tai <yuchuan at stat.berkeley.edu> wrote:
> Thanks! In your code below, to take care of the paired-end reads, is it
> correct that at least I need to set isPaired=TRUE in scanBamFlag()?

No.  The "isXXX" stuff is for filtering the data.  Assuming that you
want all your reads to be included (and not just paired reads), you do
not need to set isPaired.

Sean

> Best,
> Yu Chuan
>
> On Thu, 7 Jun 2012, Martin Morgan wrote:
>
>> 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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>>
>>
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