[BioC] [devteam-bioc] Depth of Coverage and Base counts from BAM file

[Hervé Pagès]

On 09/03/2013 12:01 PM, Maintainer wrote:
> Hi Chandu,
>
> Alternatively, you can use a combination of
> readGAlignmentsFromBam/sequenceLayer/consensusMatrix,
> to generate one consensus matrix per chromosome.
> See ?sequenceLayer in the Rsamtools package for an example
> of how to do this.

Forgot to mention that sequenceLayer() is only available in current
BioC devel (i.e. BioC 2.13).

Cheers,
H.

>
> H.
>
>
> On 08/29/2013 01:10 AM, Maintainer wrote:
>>
>>
>> Hi Chandu,
>>
>> The 'applyPileups' in the 'Rsamtools' packages will help you here:
>>
>> "An array of dimensions nucleotide x file x position.
>> The ‘nucleotide’ dimension is length 5, corresponding to ‘A’, ‘C’, ‘G’,
>> ‘T’, and ‘N’ respectively." (Taken from the 'Rsamtools' manual)
>>
>> The coverage you can then get with a function like 'rowSums'.
>>
>> Best wishes
>> Julian
>>
>>
>> On 08/29/2013 09:58 AM, Chandu [guest] wrote:
>>>
>>> Hi ALL,
>>>
>>> Given BAM file, I like to get output something like below. Any ideas?
>>>
>>>
>>> Chr     Position     DepthOfCoverage         BaseCounts
>>> chr1   14112	   14	                         	A:0 C:0 G:0 T:14 N:0
>>> chr1   14113	   13		                	A:0 C:13 G:0 T:0 N:0
>>> chr1   14114	   11		                        A:0 C:0 G:0 T:11 N:0
>>> chr1   14115	   11		                 	A:10 C:0 G:0 T:1 N:0
>>>
>>> Many thanks in advance.
>>>
>>> Best Regards
>>> Chandu
>>>
>>>     -- output of sessionInfo():
>>>
>>> R version 3.0.0 (2013-04-03)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
>>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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