[BioC] base-specific read counts

[Yu Chuan Tai]

Hi Sean,

I see. Thanks for your clarification!

Best,
Yu Chuan

On Thu, 7 Jun 2012, Sean Davis wrote:

> 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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>>>>>
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>