[BioC] base-specific read counts

[Yu Chuan Tai]

I see. So, which input arguments of scanBamFlag() or ScanBamParam() take 
care of paired-end reads? Or should I even worry about the paired-end 
natural when calculating coverage?

Thanks!
Yu Chuan

On Thu, 7 Jun 2012, Sean Davis wrote:

> 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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>