[BioC] ShortRead with BAM

[Duke]

On 4/28/10 10:17 AM, James W. MacDonald wrote:
> Hi Duke,
>
> Still the wrong list. You want Bioc-sig-sequencing.

Thanks :D. I thought ShortRead (and other NGS packages) is in 
BioConductor group too, but I forgot cc'ing to bioc-sig-sequencing group.

>
> Duke wrote:
>> Hi all,
>>
>> I am totally new to both R and BioConductor, so please be easy on me. 
>> I just updated my R package to 2.11, and installed new ShortRead 
>> package, but it seems that I am doing something wrong, and that there 
>> is some changes from ShortRead 1.5 to 1.6 (like the command format 
>> etc...). I tried to read a BAM file by creating a file as follow:
>
> You don't want the ShortRead package. You want Rsamtools, and the 
> scanBam() function. See ?scanBam for more info.

Thanks for pointing this out. I will try Rsamtools. But readAligned does 
have *BAM* type now. How can I use it?

D.

>
> Best,
>
> Jim
>
>
>>
>> library(ShortRead)
>> sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs')
>> ap <- analysisPath(sp)
>> (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM"))
>>
>> but running the above just gave me the content of dirPath function. 
>> My package infos is:
>>
>> > sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] ShortRead_1.6.0     Rsamtools_1.0.0     lattice_0.18-5
>> [4] Biostrings_2.16.0   GenomicRanges_1.0.1 IRanges_1.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   tools_2.11.0
>>
>> Anybody has any idea?
>>
>> Thanks,
>>
>> D.
>>
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>