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

[Hervé Pagès]

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.

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
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