[BioC] base-specific read counts

[Sean Davis]

On Thu, Jun 7, 2012 at 11:24 AM, Yu Chuan Tai <yuchuan at stat.berkeley.edu> wrote:
> 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?

There are situations when you want to calculate coverage based on the
extreme ends of pairs, but that would be for finding structural
variants and the like and not for determining base-level coverage.
You do not need to do anything special to read in paired-end data.  As
Martin mentioned, there is more complete handling of paired-end data
in development, but that is really orthogonal to the scanBamParam()
isPaired flag.

Sean

>
> 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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